Fonts missing in MathType EPS equations

Hope someone can help me! Have an InDesign file, originally created in 2010 using CS4. Now using CS6 to update. Original layout had a placed Word document containing thousands of MathType equations; for some of the content the writer typed directly in the body of the Word file (x + y = z); others he used MathType to create the equations, which are now linked as EPS files in the InDesign file.
Our problem is some of the linked EPS files are not showing the correct font.....where the fonts should be Times New Roman italic, we are seeing Helvetica in our InDesign layout. The preview icon next to the linked EPS image (on the left in the Links palette) is showing the correct italicized text. When I open the problem eps files in Illustrator, the font that's supposed to be the Times New Roman Ital is getting substituted with Myriad Pro. BUT when I open the problem EPS files to edit them in MathType 6.7, the italicized Times New Roman font appears correctly.
This problem is inconsistent...some MathType generated eps equations are fine and will appear right next to some that aren't (even the same equations!) Am not getting any font error messages in InDesign; have tried turning on/off Times New Roman in Suitcase and Font Book. Have tried deleting cached font files.
Again, the document has thousands of equations so can't just manually open up each in AI or MathType to fix/swap fonts. Have had some success bringing sections from original 2010 Word file into a fresh CS6 document but it's not an option to re-layout the entire document.
Any ideas? Am tearing my hair out! THANKS!

So, anyhow: you have PICT files with embedded PostScript.
It's not super-surprising to me that they are hard to read and InDesign doesn't do what you expect.
Also, they are malformed, or at least mutant, because their embedded raster image is in a different font their embedded PostScript.
Preview.app can read them if you rename them to .pict first.
It gets the fonts right.
I am not really familiar with PICT files (aka QuickDraw Picture Comments?). I just spent far too long slogging through the legacy apple reference, Imaging With QuickDraw. Ow my head hurts.
Ideally you want to mass convert these files to EPS (or some other reasonable format).
I don't know how you should do that.
Hopefully MathType can offer you a solution.
Maybe MathType is scriptable with AppleScript (I dunno, I don't have it).
That's about all I can do. Hopefully someone else can help you out.
Oh, I suppose a fallback would be to script Preview.app. It can open them and save them as PDF. But unfortunately it saves them as raster images (of high resolution) and of course they are not further editable in MathType. But it is possible to script Preview.app, so you could do a bulk conversion there.
Oh, another choice is to extract the PostScript from the PICT file by hand/magic/handwave/whatever and then doctor it so that it does work. This is actually kind of straightforward, you just replace
currentpoint 3 -1 roll sub neg 3 1 roll sub
1888 div 512 3 -1 roll exch div scale
currentpoint translate 64 8 translate
with some scale factor that works, like:
0.1 0.1 scale
Unfortunately, this seems to give...messed up font positioning:
so it's probably not the way to go. (And is that x backwards???? Umm… )
Anyhow, yeah. Happy New Year.

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