(Insert some type of fanfare music)
I have resolved the problem!
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.