Just had the same problem with a client 60 minute film she has been working on for 3 years. Our solution was to render each sequence completely, look at it and when you see a bad frame, select the clip, do something to it like move it up a line and then back down, and then render that clip. Do that to the end of the sequence, then export 10 minute (more or less) sections as Quicktime. Open a new project, put the rendered clips in a new sequence, look at it again, fix any clips that screwed up or that you missed the first time by going back to original project and fixing them and then exporting just that 10 minute section, put the new export in to the new project and check again, then output the new sequence.
Tedious but it works.
Errors might be the result of multiple version of FCP being used on the project, or??? I have only had this problem once before, and it was a project that I had done multiple revisions on over a three year period.
Anyway, interesting that you had this same problem with what seems to be a similar project.
Good luck
Peter
FCP 6.0.2
OSX 10.4.11
QT 7.3.1
MacPro Quad 3mz
8 gig ram
KONA LHe