What are the codec installed on your PC ???
Did you use Directshow to open it under tmpgenc or are you positive about the fact no directshow filter has been used ?

(Insert some type of fanfare music)

I have resolved the problem! :D

Thats all. Bye.

...Just kidding. Let me explain what I did.

Using either vobedit or this little app I found called VobUtils, I can seperate all the different streams by VOB ID and/or Cell ID. At all the locations where the synch problem would introduce itself, I discovered there was a very short stream (about 1.15 seconds long) that was providing a black screen between certain streams. Once I took them all out of the picture, synch problem was gone.

The weird thing about it for me is that the original VOB I was focused on contained the video and audio in synch, including that short stream. Once it was demuxed, the synch was screwed. The length in time of both the video and audio remained the same though. So I am not sure why this happens where it does, but I can live without knowing. Just glad to have gotten to the bottom of it.

Thanks so much for all your guys trying to help me out with this. Feel much better now that it is sorted. :D

I've seen that one before..for example, Fellowship of the Ring EE contains several black frames at the disc change spot when you join the first and second disc. If you don't remove them, you've got a sync issue right there. When you don't join the two discs, no problem.

Actually that's why I asked you to check the audio track (The Two Towers has silence in the audio track when the disc is changed) but I forgot that the video can have empty frames as well :?

Authoring protection using seemless branching. That's a possibility.