Here is the latest beta. It can demux the TrueHD audio with eax3to (during a second demux pass). Of course, it's slow, but it's better than nothing. Again, there are probably some bugs...
Also, the current input mode (BD or MKV 3D) is now saved with the preferences, so that it will be used by default the next time you open BD3D2MK3D.
Download:
BD3D2MK3D_v0.87b5.7z
(I have not verified the PTS of the subtitles yet. I have to go now, but I should have some time tomorrow...)