about that sound, bdrb doesn't change the sound volume. Check the original or your playback device. about that scene stuff, not a bdrb issue either. BDRB just recodes what's it being fed. That repeated scene is an indication of an improper decryption.
ooh and looks like the 3D support of tsmuxer is really getting into the dev stages now
http://forum.doom9.org/showthread.php?t=168539