Turisu said:

Well I can confirm my sync issue has nothing to do with VLC. To figure out what's going on at my end once and for all I demuxed all the audio files and compared the waveforms from the LD track and the BD 'fake' mono track side-by-side.

The two tracks are in perfect sync up until 00:20:12 at which point the two tracks desync and the LD track is ahead by about 120ms. The weird thing is that this is right in the middle of a scene so I'm not sure what would account for that.

Anyway the solution for me was simply adding 120ms of empty background sound at this point and now everything is perfectly in sync throughout the whole movie. :)

That's really interesting. Still doesnt explain how others are not having sync issues. Is it worth comparing the fake mono track to DB's w64 file?