Are you using your computer while encoding your movies?
Some encoding programs will use 100% CPU while they work. This, of course, depends on your computer. See how much juice the program is drawing by looking in your task manager. I mention this because I have read that overtaxing your computer during encoding can cause audio/video sync issues.
Do you have a codec pack installed on your computer? When I had one, it would cause several encoding programs to crash (or not load). Uninstall all codec packs and then try to load DVDSanta. Reinstall individual codecs as needed (I use AVICodec...free...to determine which codecs are needed).
Good Luck
Dano
P.S. Check out afterdawn.com - they've got a lot of good encoding guides.