I think you have corrupt video files. The corruption is probably happening during capture. There could be a problem with your capture device or its driver.
Sometimes corrupted files will play-back fine, until they are re-coded & rendered to final DVD format. The rendering program can get really confused, or it may throw-away bad video-frames, while keeping the audio intact. The length of the video & audio tracks become different, and you get a sync problem.
If you can make a problem-free DVD from the (unedited) ripped files, then corruption is the problem. I assume that you have some (illegal?) software to remove copy protection from your commercial DVDs?
If you're capturing directly to MPEG, try capturing to AVI (assuming your capture device will allow it). MPEG encoding requires lots of computing power, and its better to do the MPEG conversion after the video is digitized so that CPU speed is not an issue.
Also, because MPEGs are not meant to be edited, simply editing them (transitions, etc) can corrupt them. I had this problem with VS8, I don't know if it's still an issue with VS9. You may need a special purpose MPEG editor.