The problems with the XviD+Mp3+Subs.mp4 file have been solved with 1.39.829 :D
Here is a screenshot from the Notebook clip:
And for the Matrix clip (ignore the black background):
As for the vsshort-vorbis-subs.mkv file:
When no external subs are present it plays correctly, displaying the embedded subs. However when I place a sub file called 'vsshort-vorbis-subs2.srt' (notice different filename) in the same directory, those subs are used. I guess this is because it has the same prefix as the movie file. So this more a feature than a bug. I now also noticed that the embedded sub tracks also show up in the subs menu. However, after selecting one of them bsplayer keeps showing the external sub. So that is a bug.