From your description I would say the problem is probably field order reversal. You card has most likely captured top field first, but somewhere alone the way the field order has been reversed to bottom field first during encoding. Deinterlacing in the software players has reduced the effect on your PC. I suspect if you play back one of the VOBs in virtualdubmpeg2 you will see the same problem.
I don't know of a nice way to fix it without reauthoring. If you demux the mpeg out of the VOBs you can use Restream to fix the field order, but the you have to recreate the VOBs and put them back. Probably easier to just create a new menu and author a fresh with the fixed mpeg files.