I don't think his problem has anything to do with his HD partition. It is standard for VOB's to be split into 1gb chunks on DVD's. However this can be a pain for people who work with other file types such as .avi (XVID or DIVX) and .mp4 (H.264), because you need the full file to send it through many conversion programs. This is the reason I have to use DVD Shrink for this purpose. Luckily most of what I convert is TV shows and most are not encrypted, but when they are I have to run them through DVD Fab Decrypter and then into DVD Shrink.
You may ask why I don't use DVD Fab Platinum to do this in one step and the reason is simple. DVD Fab Platinum does not support 640x480 iPod with H.264. I have asked before if it would ever be supported and have not received a response.
KMEC20, I think you can solve your problem by taking what DVD Fab ripped onto your hard drive and open it in DVD Shrink. Go to the settings of DVD Shrink and uncheck split into 1gb chunks. Then select whatever you want, I go into reauther and would just select the movie. This should fix your problem I believe.