I'm thinking that somewhere along the line, the files are changing ever so slightly and corrupting.
Yeah, because if MP3toFID isn't actually changing the contents of the files (just renaming them), then the corruption has to be ocurring on the transfer or on the empeg hard disk.
But maybe the MP3 files are fine, and the problem is some sort of an issue of a mismatch between the index FIDs and MP3s. For instance, you copy all the files to the empeg and somehow there is a file there that is a playlist FID and the index FID of the same name expects it to be an MP3. Something like that.