Font ID Conflicts

TextEdit kept crashing on me when I tried saving a file, so I decided to clear my font cache and do a font validation/resolve duplicates. That problem is solved. I downloaded a trial version of FontDoctor, thinking it was a fully functional trial, but it's not. I went back to the Web site to purchase it, but don't have $70 to drop on software right now. Wondering if anyone can help me understand and resolve the following font ID conflict it found. I can't set this up the way it looks on my screen, so I'm using outline format to identify indentation.
I) Courier Final Draft
A) [Finder] /Library/Fonts/Courier\ Final\ Draft
B) [X in circle] ID Conflicts (ID# 2000)
1) Arial Narrow (Bold, Italic)
a) [Finder] /Library/Fonts/Microsoft/Arial\ Narrow
Message was edited by: Stephanie Michelle
Message was edited by: Stephanie Michelle

Courier is a standard OS X font. There's no need for another version of the same font. I would consider removing rather than disabling. The latter does not mean the system will overlook a duplicate ID problem. You don't need to delete the font, just remove it from the font folder in which it's installed.
You might also check all the font folders to be sure you haven't got the same font installed in more than one folder. Check:
/System/Library/Fonts/
/Library/Fonts/
/Home/Library/Fonts/
And don't overlook the Applications Support folders in /Library/ and /Home/Library/ where some applications install their own separate fonts. Final Draft may not install their fonts in the standard fonts folders.

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Arial.ttf
Arial Italic.ttf
Arial Bold.ttf
Arial Bold Italic.ttf
Brush Script.ttf
Times New Roman.ttf
Times New Roman Italic.ttf
Times New Roman Bold.ttf
Times New Roman Bold Italic.ttf
Verdana.ttf
Verdana Italic.ttf
Verdana Bold.ttf
Verdana Bold Italic.ttf
Wingdings.ttf
Wingdings 2.ttf
Wingdings 3.ttf
Here's where it gets a bit trickier. Office 2011 also installs a number of old fonts which conflict with the newer .ttf OpenType fonts. Delete these from the "lib" folder on your desktop. Note that they do not have a file extension.
Andale Mono
Arial Black
Arial Narrow
Arial Rounded Bold
Comic Sans MS
Georgia
Impact
Tahoma
Trebuchet MS
Without being able to see what you have left in the "lib" folder, I can't easily say what you can move back into the /Library/Fonts/ folder. So I'll list everything else Office 2011 installs that you can move back in. Office uses many of these for its supplied templates. Cambria is the default font family for Word.
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Abadi MT Condensed Light
Baskerville Old Face
Batang.ttf
Bauhaus 93
Bell MT
Bernard MT Condensed
Book Antiqua
Bookman Old Style
Bookshelf Symbol 7.ttf
Braggadocio
Britannic Bold
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Calibri Bold.ttf
Calibri Italic.ttf
Calibri.ttf
Calisto MT
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Cambria Bold.ttf
Cambria Italic.ttf
Cambria Math.ttf
Cambria.ttf
Candara Bold Italic.ttf
Candara Bold.ttf
Candara Italic.ttf
Candara.ttf
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Century Gothic
Century Schoolbook
Colonna
Consolas Bold Italic.ttf
Consolas Bold.ttf
Consolas Italic.ttf
Consolas.ttf
Constantia Bold Italic.ttf
Constantia Bold.ttf
Constantia Italic.ttf
Constantia.ttf
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Copperplate Gothic Bold
Copperplate Gothic Light
Corbel Bold Italic.ttf
Corbel Bold.ttf
Corbel Italic.ttf
Corbel.ttf
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Desdemona
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Engravers MT
Eurostile
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Franklin Gothic Book.ttf
Franklin Gothic Medium Italic.ttf
Franklin Gothic Medium.ttf
Gabriola.ttf
Garamond
Gill Sans MT Bold Italic.ttf
Gill Sans MT Bold.ttf
Gill Sans MT Italic.ttf
Gill Sans MT.ttf
Gill Sans Ultra Bold
Gloucester MT Extra Condensed
Goudy Old Style
Gulim.ttf
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Harrington
Imprint MT Shadow
Kino
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Lucida Bright
Lucida Calligraphy
Lucida Console.ttf
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Lucida Handwriting
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Lucida Sans Typewriter
Lucida Sans Unicode.ttf
Marlett.ttf
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Meiryo Bold.ttf
Meiryo Italic.ttf
Meiryo.ttf
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Monotype Sorts
MS Gothic.ttf
MS Mincho.ttf
MS PGothic.ttf
MS PMincho.ttf
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MS Reference Specialty.ttf
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Palatino Linotype Bold.ttf
Palatino Linotype Italic.ttf
Palatino Linotype.ttf
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Perpetua Bold.ttf
Perpetua Italic.ttf
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Tw Cen MT Bold.ttf
Tw Cen MT Italic.ttf
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Now open Disk Utility and run a Repair Permissions on your startup drive. Moving the fonts around will cause them to have permissions OS X doesn't like. Mainly just because you moved them back into the /Library/Fonts/ folder and it will want to change the permissions to OS X as the owner simply because of where they are.
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sudo atsutil databases -remove
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This removes all font cache files. Both for the system and the current user font cache files. After running the command, close Terminal and immediately restart your Mac.
Last step when back at the desktop. Launch Font Book so it can create a new database based on the fonts currently in the drive's three Fonts folders.
There should be no duplicates. Everything OS X and Office installs will be available.

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I may receive some form of compensation, financial or otherwise, from my recommendation or link.

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OK. I've gotten the original PDF files that were exported from CS5 and then placed into a new CS6 document and then exported from the OP. By the way, the problem is not limited to exported PDF, but also with PDF created by distillation of PostScript from CS5.
I cannot replicate the problem by simply creating a new InDesign CS6 document and placing pages into the new document and exporting.
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*     The CS5 exported PDF file(s) were edited, possibly in Illustrator or with object editing in Acrobat Pro either with native tools or third party plug-ins and then resaved with the resultant PDF file(s) placed in the CS6 document. This editing may have messed up spacing of text that used ligatures, alternate characters, old style figures, etc. even though such text was not directly edited.
*     The CS6 exported imposed spreads were subsequently opened in Illustrator or some other third party trapping engine and resaved with the Trapped True key set. In the process of resaving the file, problems per (1) above occurred.
Conclusions:
(1)     Whether PDF/X-1a or PDF/X-4 was used for export anywhere in this process is irrelevant. The designs in question didn't use any transparency or color management. Furthermore, no CID-encoded fonts were involved and no font name conflicts were involved. However, the fonts used in the original InDesign documents were OpenType CFF fonts with extended character sets which were in fact accessed for ligatures, superscripts, subscripts, etc.
(2)     Previously non-disclosed steps were used in the workflow between the CS5 export and the resultant files I got to see. Using Illustrator as a PDF editor or as trapping software for PDF files in general is a possible / likely cause of the problems. If not Illustrator, then some very defective PDF workflow software for trapping and/or editing was used.
(3)     Although InDesign is not designed as an imposition tool, the fact is that it is used for amalgamation of content such as magazines, journals, etc. where ads and other content as PDF (and other formats) is placed within InDesign pages. This appears to be working correctly and is not the source of the problem.
The OP is dealing with problematic workflow, but not with InDesign problems.
          - Dov

Font ID Conflicts

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