Hi
vico1, don't know if I'd exactly consider myself an insightful mind

, but I'll toss in a few pennies for what it's worth...
If your audio de-synch was at a constant rate throughout the entire movie (including from the very beginning), then fixing it would be as easy as changing the audio startup delay in BBMPEG until it matched (but this doesn't seem to be what you're describing). How long does it take before the audio/video de-synch is noticeable to you? (i.e. after the first episode, halfway through the first episode, the start of the 3rd episode, etc). One way to "
solve" the problem would be to break the file up into smaller parts.
Since Animatrix is actually 9 episodes with about 4 or 5 seconds of black "nothingness" seperating each one, I'd say to just use the "start second" and "end second" functions under the General Settings Tab of BBMPEG to mux each episode separately, rather than muxing the entire movie into one file. Use a media player to watch your de-synchronized file and write down the start and stop times for each of the episodes...you'll also probably want to make sure to include a couple seconds of the blackness that separates the episodes (also keep in mind that these times given by your media player may not be 100% precise, so you
may need to play a bit to find the exact right start/stop points to use in bbmpeg). For each episode or file you mux, just change the audio1 delay accordingly in the "Startup delays (ms)" area of the Program Stream Settings Tab of BBMPEG until the video and audio of your output file match up (keep in mind that milliseconds are very tiny, so you probably won't notice a difference unless you make a substantial increase/decrease).
Then you could just burn all 9 episodes as individual tracks with a 0-second pause/gap in between them so they will still play seamlessly, or I suppose you could also try rejoining them all into 1 file by using TMPG's MPEG Tools (though this
might potentially create some synch issues as well, so I'd just burn them as 9 separate tracks myself...doing this would also give you the benefit of easily being able to skip to the next episode during playback by simply pressing the "chapter" or "next" button on your player's remote).
It's really not as difficult as that clunky/wordy explanation may have made it seem

(heck,
I've done it before, so it can't be
too difficult!

). Hope it helps.
Good luck,
-d&c