Missing Font, But Font Isn't In the Document

Question

Hello,
We're all using FrameMaker 10 on Windows 7.
My client and I are receiving the good old missing fonts error message, specifically:
The "ITC Stone Serif Std Medium Ital Italic" Font is not available.
  It will be replaced by "Times New Roman Italic".
The "ITC Stone Sans Std Semibold" Font is not available.
  It will be replaced by "Times New Roman".
First, the fonts are installed.
Second, Remember Missing Font Names is turned OFF. (Unchecked, cleared, etc.)
Third, the fonts are NOT in the document. I have saved the document as MIF. I have searched for the font names. Nothing. When I open the MIF file in FM, I don't get an error. But I save it as a .fm file, open it, and I receive the same error messages.
We don't use these fonts. We don't want them in our documents. I'm doing a massive clean up to get rid of old formats. About half of the files do not have any problems, but half do. I have tried everything:
- Generating a list of fonts. If the fonts are found, then I go in and manually apply the Default Para Font. Usually, doing this removes the font from the list of fonts. However, I still get the messages.
- Importing formats from a known good file. 
- Editing the MIF, to the point of removing the entire paragraph, character, font, and table catalogs. (I started by deleting references to ITC Stone x, then went on to the more drastic measures.)
- Changing the default printer.
- Copying the text and pasting it into blank files based on known good files.
- I tried editing the maker.ini file to substitute fonts directly, but that didn't work. I may have been doing that wrong, though. 
I've got over 10 years of FM experience, and I've never encountered a font problem that editing the MIF couldn't fix.
All of the documents came over from Frame 6. They're all in the same book.
We need to be able to work on the book file as an entity, without having to open the files that contain errors and leave them open.
Does anyone have any ideas?
Thank you very much!
~Robyn

Answer 1

I found the problem, but I'm not sure why it was a font problem to begin with:
Unresolved cross-references.
FM couldn't open all of the files in the book. Therefore, it couldn't update cross-references. It "thought" cross-references were unresolved.
I figured this out by deleting one page at a time from a Bad file. Then, I deleted one paragraph at a time from the Bad pages to determine that the cross-references were causing the problem.
I was cleaning up the book - deleting paragraph, character, cross-reference, table, and conditional text formats and master and reference pages. I then imported formats from a known Good file. The more files FM could open without errors, the fewer font errors I received. After I was able to generate/update the book, the font errors were gone.
Some of the font calls were on a reference page that was found only in select files. However, one would think that would show up in the MIF.
My best guess is that FM couldn't update the cross-reference formats without updating the cross-references, so it "thought" the text was still in the wrong font. That begs the question: Which came first, the unresolved cross-references or the missing fonts?
Of course, it doesn't explain why FM was complaining about a font that is installed.
Thank you everyone who took the time to answer. I'm sure this won't be the last time I run into this problem, and now I'll have a lot more knowledge for next time.
~Robyn