Fonts Incorrect when using compressor

When I encode my .motn file straight from Motion, the fonts show up correctly in the finished quicktime. However, I've got about 62 of these motion files that need to be batch encoded, but when they come out of Compressor, the fonts display incorrectly...as if the font is not on my machine and being substituted.
I've checked several of the motion files and the fonts they are using are installed on my system. What would cause this to happen?

Ok, now I'm really stumped. So I took Patrick's suggestion and reinstalled the fonts system-wide. I checked the fonts were working correctly by launching a couple of the motion files, checking the fonts, then saving them.
I then trashed Compressor's pref files (and FinalCut's pref files just for fun). Then I repaired disk permissions and rebooted. Once back in, I launched Compressor and loaded up two of the Motion projects. After choosing the appropriate encode preset, I double checked in the preview window and the fonts were dispalying correctly. Yay! So I submitted the job and waited. I opened the final quicktime file and the fonts are INCORRECT. What in the world??
So, to recap: fonts show up correctly in Motion, they show up correctly in the Compressor preview, they even show up correctly in the timeline of FCP. But exporting from Compressor results in the wrong font and exporting my sequence from FCP crashes my system every time. I'm so confused.

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Message was edited by: Ricardo Javier

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Fonts Incorrect when using compressor

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