Lord of the Rings (Extended Edition) Sync Issue

[kshawkeye]

Okay, I have been all over doom9, and prettymuch all over the internet trying to find a solid solution to this, and I apologize if there is one out there that I didn't find, just show me where it's at. After trying to encode The Lord of the Rings (Special Extended DVD Edition) - The Fellowship of the Ring, with Gordian Knot v0.35.0 two times, and running into sync issues with the second half of the movie. The problem is due to combining two DVDs in DGIndex and then a few frames being dropped in the transition from one DVD to the other (at least that's what I believe it might be). So my question is, how can I encode a two part DVD into a single .AVI file, with perfect sync, using Gordian Knot v0.35.0? Thanks so much for anyone's help, and once again, I apologize if there is another forum out there that has covered this, I couldn't personally find it.

EDIT: Oh, and by the way, I ripped the VOBs with DVDFab v6.2.1.8, if that is helpful in any way.