Seamless branching creating problems with audio-sync (blu-ray)?

I’ve noticed that when I backup a blu-ray movie that has seamless branching to .mkv using MakeMKV, the WDTV Live seems to stumble where each new segment starts, and from that point on, the audio is slightly out of sync (and gets progressively worse if there are more segments).

Anyone have an suggestions on this?  Will it work better if rip the film differently?  For example, I could make an .m2ts instead with tsMuxer.

And I don’t think it’s limited to seamless branching.  Some blu-rays, like the new Twilight release (Breaking Dawn part 1), have the “fake” movie streams on them.  And by doing this, the manufacturer has created the streams with like 20 segments.  This wreaks havoc on the the audio sync.

Just wondering if anyone else has run into this, and if so - any workarounds?

If you rip the right title in MakeMKV after having checked out the proper playlist in TSMuxer or something you should get an mkv that’s in sync.