I checked my mux. You're correct it goes in and out of sync by 100/200ms after a while.
Dark Jedi or Stendec files however sync perfectly. if there's a difference by the end, it's probably of tenth of milliseconds, hardly noticeable.
That's crazy because Dark Jedi rip was synced to the old Blu-ray, which used the same master as the old 2001 DVD which had the mono track.
You know what, it might explains WHY the mono track from the DVD is not included on the new master, and also why it isn't on the old Blu-ray.
It might be it's kinda botched by time breaks that they couldn't fix based on the files they had.
There's no reason it shouldn't sync, except if seamless branching has something to do with it, (as the DVD have tons of hidden features and branching and stuff), and I recall when I imported the movie in mpegstreamclip, it found like a hundred time breaks). Maybe the mono track have "time breaks" that you and I and they couldn't fix with mpeg streamclip that render it difficult to sync to the HD raw files of the old version and the new one.
They probablly thought that resyncing it to the Blu was too much work.
Of course, they could have asked Dark Jedi for a synced mono file for free...