Cross-reference mixup after package

Hi,
I've got a question regarding InDesign cross-reference.
Here's the background:
The original source is stored in F drive.
Packaged source is stored in C drive.
For each of my drafts, I need to attach the packaged source with the PDF.
I have 10 cross references in a 100 page document.
The question is this:
When I package the InDesign files, I assumed that my cross references will be updated to the InDesign files in the packaging directory.
But when I checked them out, the cross references were still linked to the original source. So I had to manually update each cross reference to the packaging directory.
Although the PDF works fine, I have some concerns about this situation.
Does any one else had this problem? If so, are there any solutions to this issue?
Any help is greatly appreciated.
Thx.

Books are funny creatures. Another thing that confuses a lot of users is that if you make a copy of the .indb file and all the component .indd files, the copied .indb does not point to the copied .indds, but retains the links to the original locations.

Similar Messages

Cross references corrupted after placing Word document into an InDesign document

I am placing a word document which contains cross references to headers and captions/figures within the document. They seem to be fine and function correctly in the Word document, however, after I place this word doc into my InDesign doc, I take a look at the cross references panel and notice that the cross references have been corrupted. It is wrapping the wrong portions of text from the cross reference destinations. See screenshot for a visual of how the cross references are malformed. For example the 7th cross reference in the list should say Framework Details, not "Framework Detai
InDesign Cross References Panel - showing malformed bits of text
Another visual of this issue can be seen if I view the text frame in Story Editor view, see below. You can see that the cross reference source tags (blue arrow like symbols) are wrapped around the wrong portions of text. The blue tags shoud be wrapped around Framework Details and 52
InDesign Story Editor
You can see below as to why I think the cross references are fine in the Word doc, you can see the same cross reference I used in the example above in the word doc and it is wrapping the correct portion of text:
Word - showing cross reference is formed corerctly
Why is this not being maintained after placing this file into InDesign?
Also I am not performing any cross reference updates after I import, this problem occurs immediately after the place of the doc.
Why would InDesign be having difficulty in importing these cross references? I have set up a simple test Word document with cross references to headers and figures in and they have imported fine. What could be wrong with this other particular word doc that would be causing this "corruption" of cross references? This is not only causing my cross references to break visually and lack the update capability but also I cannot export the InDesign doc to an ePub as it keeps crashing. I believe from my reading on the web that if there is only one broken cross reference source i.e. the cross reference destination that it is trying to link to is missing, then the export to epub will fail. So this is causing a massive headache for me at the minute.
Is there anything I could be looking at in the Word doc to try and figure out why the porblem is occuring in the first place?
If anyone has any tips or a possible solution to this I would really appreciate it. Even better if someone knows the reason why this is happening I can tackle it from the source and prevent it happening time and time again.
Thanks, Dave

Only bad experiences, Peter ...
I've seen this character shifting before on numerous occasions, both with cross references and with hyperlinks. (It's especially funny with hyperlinks, 'cause you can see that the outline box shifts one character at a time per each next link...)
The thing is it's not just limited to hyperlinks and cross refs. Dave's screenshot doesn't show bold, italics, or other local formatting, but it's a fair bet these are off by a couple of characters as well.
Dave's experiment of making a "minimal" Word document to confirm it's a persistent bug didn't work. I found the same thing: either a document comes in fine, or everything is foo-bar right from the start. There must be some internal Word code that InDesign forgets to count as 'a character position'. Without delving into the Word file with some very advanced tools, it's anyone's guess what code that would be.
I can only offer the one solution that works for me: in Word, remove all hyperlinks (which is what Word uses for internal links as well as for external ones) and convert all cross-references to text. Then, if the file finally imports fine, re-build them in InDesign. It's a cumbersome workaround, but slightly better (only just) than checking each reference, delete, rebuild, check next -- etc. (And with that the chance that your other text attributes are also off.)

Why is a single Cross Reference text turning red after doing an Update?

After updating a large book in FrameMaker10, the same cross-reference made in a couple of chapters is turning to red text. It is set as Heading 2. I tried to deleted the heading and re-typing it. I tried to change the style to Body and back to Heading 2 but all references to it are turning to red text after I update the book. Any idea what is wrong and how do I fix it? I am using unstructured version. See image.

Apply a Character Format of Default ¶ Font. Then re-apply the desired Paragraph Format. If the red goes away, it was either a Character Format that had been applied or a local color override. If the red is still there ...
Look at the Special > Cross-Reference > Format > Definition itself. Look for any <character-format-name> and see if any of those have a red Color defined in their Format > Character > Designer. If so, remove that building block from the definition [Change] [Done] [Replace].

Relinking Cross-References after Renaming Documents

I have a problem where I have created a book containing 14 chapters. Each chapter has a reference to the language of the book i.e. GB in the document title, we now want to translate the documents, so have copied the book, and chapters, renamed the document with an FR in the document titles, ready to send of to the translators.
The trouble is all the cross references are still linking to the GB book. Is there a way of re-linking all the cross references to the FR documents? Or is it a case of going to each cross-reference and re-linking to the same piece of text but in the FR book.
Can anyone help?

tRawc wrote:
I have a problem where I have created a book containing 14 chapters. Each chapter has a reference to the language of the book i.e. GB in the document title, we now want to translate the documents, so have copied the book, and chapters, renamed the document with an FR in the document titles, ready to send of to the translators.
The trouble is all the cross references are still linking to the GB book. Is there a way of re-linking all the cross references to the FR documents? Or is it a case of going to each cross-reference and re-linking to the same piece of text but in the FR book.
Can anyone help?
No help here, at least no help in providing some magic. Cross-file cross-references seem to depend on the name of the file that contains the cross-reference "destination" - the text that's captured and displayed at the "source" - the location where the cross-reference is inserted. I'm using quotation marks here because some folks think of the stuff you capture as the cross-reference source, and what's displayed at the cross-reference insertion point is the destination in their view. IOW, they're opposite uses of the term. InDesign's nomenclature is based on the hyperlink model, where you create a destination somewhere and you act on it by pointing to that destination from where you insert the link to it, AKA the source of the action. At least that's my guess.
So, changing file names loses the connection.
Internal cross-references - within a single document file - are maintained when the file's name is changed.
You can relink cross-file cross-references for files that are moved to a new folder. In the Cross-References panel, select a "missing" cross-reference that displays a question mark in a red circle, then from the panel's fly-out menu, choose Relink Cross-Reference, and browse the directory. If all the cross-file cross-references in the file whose cross-references point to files in one directory, relinking should restore all the links. If some cross-references point to files moved to other directories, you'll need to browse to each of those directories.
With a book, if all the missing cross-file cross-references for all the book's component files were all moved to the same folder, relinking one missing reference should relink all. If some missing cross-references point to files moved elsewhere, you'll need to browse for each of those directories.
HTH
Regards,
Peter
Peter Gold
KnowHow ProServices

Links to FM Cross References do not work in Generated PDFs

Windows XP Professional SP2, FrameMaker 7.0p576, Acrobat Professional 8.1.2.
I have multiple volumes that are intended to ship together. So, for argument's sake, I have Book_1.fm, Book_2.fm, Book_3.fm.
Within Book_2.fm, I create cross-references to Book_2.fm and Book_1.fm.
When I generate the PDF files for all three books (using Frame's Print Book, Printer set to Adobe PDF, Generate Acrobat Data so my bookmarks are generated as links), Book_2.pdf's cross-referenced links to within Book_2.pdf work perfectly. However, Book_2.pdf's cross-references to Book_1.pdf result in the following message:
There was an error opening this document. This file cannot be found.
The problem occurs whether the books reside independently, as a single combined PDF file, or as a PDF package (single combined and package both generated after the three individual Book_x.pdf files exist).
I have kept all PDF filenames identical (minus the extension) to the FrameMaker .book names.
Thanks for your input.

Sandra,
This is an explanation and NOT a solution. When you create a cross-reference to another file, you have to have the file open. Apparently, Frame sees a file in a different book as just a file; it seems to have no way to know that it is part of a different book. Hence, the link points to a chapter name, not a book name. Again this is just an explanation.
I do not know how, or if there is a way, to do what you want to do, other than edit the links after the PDFs are created, which I am sure is not what you were intending to do.
Maybe the gurus on these forums have a way to do it.
Van

Cross references not picking up character styles in source text

I'm getting some annoying odd behaviour with cross references in Frame 12.
I have some tables, where the paragraph style in the cell is called "Cell Body" (nothing odd there).
Quite a few of the cells only have one word in them, and that word is set to courier font with a character style (called "Code").
Then, elsewhere in the document, I am referring to this text using cross references. I am referencing the paragraph style Cell Body, and the cross reference format applied is like this "<hyperlink><$paratext><Default ¶ Font>"
"hyperlink" is another character style that makes the text go green.
So, the cross reference out to take the text from the cell (in Courier) and reproduce it, coloured green.
However for about half of these cross references, it isn't picking up the Code character style in the source text, so the cross ref is just green, no green courier.
Things are further bamboozled when I output to HTML Help.
In the CHM file, the cross refs which appear to work OK (green courier) are now just courier.
The ones which failed to pick up the courier look the same as they do in Frame (just green).
Any ideas as to what's going on?
I've tried troubleshooting by clearing the cells, reapplying the para style and default character style, then reapplying the code character style, then replacing the cross reference - which sometimes seemed to fix it but didn't always.

Arnis Gubins wrote:
Using two character tags in-line together (a la <hyperlink><Code>) is asking for trouble. IIRC, FM doesn't re-apply these in order on an update and depending upon how they are defined (and what is set to AsIs), the outer one usually wins. .
So why does the blimmin' dialog invite me to do precisely that, by providing me with a list of all the character styles I have, and allowing me to select as many of them as I like??? /sulks/ Indeed, if Frame still shipped with a printed user guide instead of stupid "optimised for viewing on iPhones" online webhelp nonsense, I suspect I might very well be able to find an example in the manual of using multiple character styles in that dialog! If it doesn't want you to use more than one, why doesn't it grey out after you add the first one? /sighs/ The concept is called "cascading styles", it's a fundamental web paradigm! And it works in the main body text - why not in Xrefs!
Also, I have been very scrupulous to keep my character styles orthogonal so none of their AsIs's mash each other up.
But, rant over, I shall follow your splendid suggestion for a "Code Hyperlink" style.
Arnis Gubins wrote:
Also, x-ref formatting may behave differently in the new Publishing modules depending upon ....
...Depending on how badly designed and buggy this new Frame12 feature is, I should say! The Publish module should not randomly stop behaving in a WYSIWIG manner in completely undocumented fashion just because Adobe couldn't be bothered to code it properly. /sighs/
Frankly, for my current project, I've given up trying to jump through hoops for Publish - I'm concentrating on getting the Frame source right and assuming these quirks will be fixed in Frame 13 (or 14, depending on how superstitious they are). Because if I put in ad hoc workarounds for them in Frame 12, I (or a colleague) will only have to undo them later when they're fixed, and by then we'll all have forgotten what the original problem was.

Cross reference stream

Hello!
I'm in real trouble, and I think that the answer is very close to me, but I can't get it by myself...
Here is my problem:
I'm currently improving the PDF parser that I've made, adding support for cross reference streams. After a careful reading of the ISO 32000 specification (with PDF 1.7 in background), I've wrote a piece of code that decode the stream and build the corresponding objects (I use Java).
But the decoded values are meaningless, and I don't understand why!
The data are like that:
filter predictor: 12
encoding : Flate
fields length : 1 2 1 (this is the W entry values)
column size : 4
I assume that there is one color per pixel formed by one byte.
First, I 'deflate' the data, then 'unfilter' them. Both operations look ok as I've made test for the Flate encoding (ok), and the for the filter I've use it with PDFBox source (and my work unfiltered well what PDFBox filtered...).
Note that I compared my outputs with those produced by PDFBox, and they are the same... Something may be wrong in the parameters I use, but I no idea now...
I think I missed out something as I read incorrect data as entry type 18...
I don't know where to go now, after a whole week of work!
If any have an idea, I'd be grateful to hear it!

This is ready algorithm to read PNG predictor styled Cross Reference Stream:
1. You need to read from PDF three variables: /Columns 5/Predictor 12 and /W[1 3 1] and of course stream
2. Deflate (encode) stream via zlib (without passing anything more than stream)
3. Divide encoded stream to rows, but length of each rows must be one bigger than columns variable (in this case is 6) because first value is type xref row
6. rows without first row go to UNprediction with this algorithm:
def self.do_png_post_prediction(data, bpp, bpr)
        result = ""
        uprow = thisrow = "\0" * bpr # just zero fill (byte zero - not char zero)
        ncols = data.size / bpr
        ncols.times do |col|    # just for each rows
          line = data[col * bpr, bpr]
          predictor = 10 + line[0]
          for i in (bpp..bpr-1) # just for each values of row without first value
            up = uprow[i]
            left = thisrow[i-bpp]
            upleft = uprow[i-bpp]
            case predictor
              when PNG_NONE
                thisrow = line
              when PNG_SUB
                thisrow[i] = ((line[i] + left) & 0xFF).chr
              when PNG_UP
                thisrow[i] = ((line[i] + up) & 0xFF).chr
              when PNG_AVERAGE
                thisrow[i] = ((line[i] + ((left + up) / 2)) & 0xFF).chr
              when PNG_PAETH
                p = left + up - upleft
                pa, pb, pc = (p - left).abs, (p - up).abs, (p - upleft).abs
                thisrow[i] = ((line[i] +
                  case [ pa, pb, pc ].min
                    when pa then left
                    when pb then up
                    when pc then upleft
                  end
                ) & 0xFF).chr    # AND 0xFF is very important, without this values growing extremely fast
            else
              puts "Unknown PNG predictor : #{predictor}"
              thisrow = line
            end
          end
          result << thisrow[bpp..-1]
          uprow = thisrow
        end
        result
      end
   7. Take bytes from UNpredicted rows, and in this case
   1st byte first byte is type
   2nd byte
   3rd-5th - is this what You want - offset in decoded PDF to objects (Xref table): offset = 2^9*5th + 2^8*4th + 3rd

Cross reference in ID CS4 goes to wrong destination in Acrobat

I am creating a 108-page document in ID CS4 with lots of cross references (a new feature in CS4 after using the scripting work-around in CS3). I created a new cross-reference type which is only the page number of the destination in an invisible box.
Now that the document is finished, I created a PDF. The version of Acrobat on my PC is Acrobat 9 Pro Extended.
Most of the cross-references work as expected. A handful, though, while they show the correct page number in the text, when clicked in Acrobat Reader take the user to the wrong page. For example, the text says "see page 88" but a click takes the reader to page 99.
I have opened this pdf in Reader on multiple PCs: same problem. I have erased the old X-ref and re-added it: same problem. I tried installing the recent InDesign 6.0.1 update and replacing the X-ref and re-exporting to Acrobat: same problem. If I temporarily use a different X-ref type that includes the paragraph text, I see the correct text. Bottom line: everything seems OK EXCEPT when clicking in Reader.
Any thoughts on what to try to make this problem go away?

Try opening the PDF in Acrobat, and examining the links with the links tool. That may help you figure out the problem. It will show the specific text anchor to which the link is pointed. From my experience, it just references to a page number, unless you link to a specific text anchor within ID.
I had a similar problem in Framemaker, and I couldn't resolve the issue unless first deleting the marker from the destination and letting FM regenerate it.

Cross-reference marker ID

Hi everyone,
Has anyone worked with duplicate cross-reference markers before?
My question is, is the uique number in each marker text the same if multiple markers exist in the same location?
Thank you for your help.

You can find the markers by either doing it in a brute force manner using the Find > Marker of type (and have the Marker window open to see the contents) or by using a MIF version and using a text editor to search for the MText right after a <MType 9> entry. The MText would be the duplicate and the Unique ID entry would be two lines further.
The general structure of a Marker in MIF is as in the following example:
   <Marker
    <MType 9>
    <MTypeName `Cross-Ref'>
    <MText `37042: Body: At vero eos et accusam et iusto odio blandit praes'>
    <MCurrPage `1'>
    <Unique 998385>
   > # end of Marker
Cross-refs target the MText line using a <XRefSrcText ...> entry that is the same as the MText content.

Cross Reference, Paragraph Style conflict?

I'm created an epub file and have a cross reference for one of my chapter titles. When I export it to ADE the final product has the cross reference in the file but the paragraph style for the text that I linked lost all of it's styling somehow. The paragraph style is supposed to be centered and have space after it but it is completely gone but the code is still in the xhtml file.
I have opened the xhtml file and cannot see where the issue is. Has anyone else had this problem exporting from CS4? If so, how do you fix it?
Thank you so much!

According to the FM7 Help, the variables for background text frame use might be:
<$paranumonly[paratag]>
to pick up the first instance on a page, and
<$paranumonly[+,paratag]>
to pick up the last.
The "+," bit is the key. I've never tried it myself.
This presumably also assumes that the paras of interest all have the same format name.

Cross-reference tag errors in Trados preventing MIF creation

Our Spanish translator provides files from translation memory with unresolved cross-reference text in English; when we update the book the cross-references are translated to Spanish and the page numbers are also updated within the cross-reference text. After our DTP process, when we return the files to the translator to update the translation memory, he gets a misalignment in the tags and Trados prevents him from creating a MIF file. Trados won't let him ignore the cross-references. We're using unstructured FrameMaker 2009 and he has Trados 2007. We're in the midst of a deadline for a project due next week and he wants to charge us an enormous fee to fix the tags manually. Can anyone suggest a solution the translator can use? I'm a newbie forum user, but I checked the FAQ and did not see anything. Thanks! Sue

As far as I know, FM cross-references (which came into Trados via MIF and S-Tagger) are handled as placeables. I suppose the mismatches stem from a "placeables differences penalty", which by default is 2%, even for otherwise exact matches.
A possible solution could be to impose no penalties for placeables in Trados, i.e. set the placeables differences penalty to 0%. But be careful, this may overshoot the mark, as there might be relevant differences in placeables that must be reviewed. I'm not aware of a setting in Trados where you could specify this more selectively.
Johannes

Cross Reference incorrect syntax

Trying to create a partial text cross reference using the suggested code:
<fullPara delim=”:” includeDelim=”false”/>
However, InDesign (CC) is giving me an "Incorrect Syntax" message.
Ideas?
Thanks.

@Sandee – after experimenting a bit with all kinds of quotes, I find the syntax for cross references a bit strange.
Here is a screen shot from my German InDesign CS5.5 v7.5.3. on OSX 10.6.8.
It is showing the code for "Full Paragraph and Page Number" by *default*.
Note the curly opening and closing quotes in German style.
And note, that there are no quotes around:
<pageNum />
The code is still correct, if you are not using quotes at all in this example…
Uwe

Cross reference markers are deleted for content in text insets

Cross reference markers are deleted for content text insets. I currently have a chapter that is built from several Import by Reference files. I added an introductory paragraph with cross reference links to heading 2 titles in these text insets. Everything works and saves normally, although the cross reference markers disappear from the chapter when files are checked out a few days later. An extra Heading 2 is also added to the end of the document.
Steps to reproduce:
1. Create a chapter composed of several text insets.
2. Create a list of cross references to headings in these text insets at the beginning of the chapter.
3. Check in/check out the files from a source control product.
What went wrong?:
The cross reference markers are gone, resulting in broken cross references. An empty Heading 2 is also added to the end of the document following the final text inset
What should have happened?:
The markers should remain and the heading 2 tag should not be applied to the document.
Product version:
Product: FrameMaker
Version: 7.2
Platform information:Windows XP
Hardware: Dell Latitude D620
OS Version: Windows XP Professional Version 2002, Service Pack 3.
RAM: 1GB

Thanks for the information, Van. We did try several techniques including adding the insertion point immediately after the text inset before the normal paragraph tag, but none seemed to consistently work. I will investigate this scenario futher, though, in light of your comments.
We have managed to determine a workaround for this issue by avoiding a string of text insets. For some reason, using multiple text insets without separating them with normal text causes most of the problems after we add the files to our source control system. The situaton is not ideal, but it does work for the time being anyway.
Steve

Cross-References coming from Word in FM 7.2

Hi Folks,
I have a problem with the Cross-References. I create an EDD and Read/Write rules, and generate a conversion table. With it I'm converting all the my documentation in MS Word to Structured FM 7,2. It works well, but there two main problems that I can't solve. I spent a lot of time reading the Structure application Developer Guide, but I can't find a solution.
First one is a minor problem that I can solve with a script but, maybe I'm doing something wrong on FM and it is easy to fix on the conversion table. When I apply the conversion table it generate without problems the RootElement, and apply tags for the paragraphs and Character formats, but I can't do that put other tags that are not related with text. I mean, my DTD need this structure:
<book>
<body>
<heading1>xxxxx</heading1>
</body>
</book>
and I obtain it:
<book>
<heading1>xxxxx</heading1>
</book>
I don't know if I can modify Rules, or EDD or Conversion table, to add the intermediate tag when use Structure Current Document
Second one is a blocking one. I generate the XML with the tags and fix any problem on it. It works great and I obtain a XML :
<book><heading1 Id = "i1003066"><bookmark
type = "38548: Heading 1: 1. This is the title"/>This is the title</heading1>
<paragraph>This is the text of the Title <reference Idref = "i1003066" type = "Page"/> and it bla bla bla</paragraph></book>
But when I try to re-open the XML with my structured application I obtain a log error:
"Error at line 17, char 31, Message: ID attribute 'i1003066' was referenced but never declared"
and a warning about cross-references missing (they working before save it as XML). File open and all is fine, except that references are missing and when I try to update the Reference dialog box to find other file is open with this message:
1 Unresolved Cross-References to File: Current
And ask me to find the "Current" file where point the reference. All the references in the document appears missing.
Must I have two set of files, one FM for generate the PDF, and the XML for generate the help with my XLS? It is not possible re-open the XML on Framemaker and don't lost the references?
Thanks for your help.
Regards,

Hi Van,
You wrote:
>> You need to DELETE "Xref" . . . This states that the reference element is a Frame cross-reference element; you should not include another name.
That may or may not be true. If the element names are different in the XML (DTD) than FrameMaker (EDD), this is the mechanism by which you translate names. It may be that in this case, the EDD element name is Xref, but the DTD element name is reference.
You also wrote:
>> Maybe this will help clear things up, but it may be unreasonable to expect that cross-references in Word will translate cleanly to structured FrameMaker.
In this case, I couldn't agree more. Esperanzas, I would recommend that you limit your faith in the conversion process, because there are many variables that will likely get mistranslated. Unless you are willling to do some programming with the FDK to clean up afterwards, I would expect that all cross-references should be recreated manually after import.
Russs

FrameMaker 11 trial version crashing on save and cross-reference insertion

Hi everyone,
I've recently started a new position. My prior background was heavily DITA, and I'd describe my FrameMaker experience as late beginner or early intermediate. The new position uses FM exclusively though, so I've been on a steep learning curve lately.
I'm using the trial version of FrameMaker 11, downloaded about two weeks ago, until the PO for my full FM 11 license is processed. I'm working in book and document files that have been upgraded, I believe, from FM 9 to FM 10 and then from FM 10 to FM 11. All of my colleagues are still using FM 10, with a mind to upgrade to FM 11 in the spring as our new budget comes through (I am, so to speak, the FM 11 guinea pig for the group).
My workstation is a brand new HP Elitebook laptop running Windows 7 64-bit (I believe our IT department downgraded it from Windows 8). Windows is fully up-to-date. My trial version of FM 11 is 11.0.1.382 and also up-to-date as of this message.
My issue: FM 11 randomly crashes several times a week, sometimes once a day or so, sometimes when I try any of the following:
Saving all files in a book (using Shift + the File menu command)
Saving individual document files (generally using the Save icon in the tool bar)
Attempting to insert a cross-reference (placing the insertion point within the document, then opening the Cross-Reference tool in the right-hand side bar)
The crash takes the appearance of FM freezing for several seconds, then the dreaded message window opening with the words "FrameMaker has detected a serious error and must quit", with columns of error codes below.
I've googled and binged and not found anything for this issue in FM 11, so I thought I'd post here. I have tried the following, based on somewhat similar discussions I've seen for crashes in earlier versions of FM)
Mif-washing the files
Working in the Structured FrameMaker interface instead of the Unstructured
Neither of these has worked. FM 11 trial continues to crash. It doesn't happen often; I'd say that I'm able to successfully able to perform the above tasks 20 times or so, with the crash on the 21st. But on a busy day, that's a few crashes a day.
To mitigate damage, I have autosave set to every two minutes and gotten in the habit of only having one or two documents open, instead of all in a book, to minimize the number of recovery files I need to process.
After one of the initial crashes, I did as Adobe asked and forwarded the crash report to them for troubleshooting.
My colleagues are watching all this very closely, and my troubles might influence our decision to upgrade from FM 10 to FM 11. So any insight into this issue would be appreciated!
Cheers,
Eric

Eric,
The multitude of unesolved x-refs may due to the font issues when updating the book. During an update, if the files aren't open, FM tries to open them in the background but if it encounters an error like a missing font, it skips the file and then any x-refs to that file are unresolved. This can cascade to make things look really worse than they are.
What is your default printer when you start FM? It should be the Adobe PDF prnter instance. If not, then you might want to insatll the Sundorne SetPrint utility (http://www.sundorne.com/FrameMaker/Freeware/setPrint.htm) thta will automatically set this for your FM sessions only.
One other place where fonts can hide is in table definitions. The catalog stores the font information (and not just the explicit paratag) of the cells in the header and first row. As Jeff mentions, you need to check the MIF file in detail. An excellent tool for quickly browsing your MIF is Graham Wideman's Mifbrowse (http://www.wideman-one.com/gw/tech/framemaker/mifbrowse.htm).

Cross-reference mixup after package

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