Here's what i'm gonna do:
Take my AVI's with my PocketDV2 to CF.
Transfer the Movies to my computer.
Convert to MPG with:
avi2mpg1
http://www.mnsi.net/~jschlic1/
OR
download AVIEdit:
http://www.am-soft.ru/aviedit.html
and try to reprocess the AVI files with a different codec.
I'm sure between these two methods something will work.
I'm at work atm, will try later and post results.