Interesting, i'm not too sure if this'll help or anything, but you could try to open the file into some sort of movie editing program and re-save it or fiddle about with it somehow.
I have Windows XP and it comes with a program called Windows Movie Maker. I have played around with it once or twice and you can chop and change the order of frames around with it and add in your own sound etc. You may be able to find bad frames and remove them. However I did find that it altered the quality of my pictures when it changed from frame to frame, but then again that was probably something to do with the file compression.
There is also a new version of it on the Windows update site, Windows Movie Maker 2. Haven't used it so don't know what more it has to offer. There are probably better programs out there to edit the file with though.