I used to have subtitles for my MKV files. They went away. The subtitles are present when I play them directly. I cannot get subtitles for Saki (encoded with Xvid or h264) nor Maria-sama ga miteru (h264). I have tried backing up from the test builds I was downloading (335, 339 & 345) with no change.
FFmpeg version 0.5-svn17737+3:0.svn20090303-1ubuntu6
java version "1.6.0_13"
Ubuntu 9.04 (64 bit Server) -- I am pretty sure it is the 64 bit flavor
The Debug file showed that the subtitles were "und" so I added that, but now the sound is "tinny" I tried both stereo and 5.1 settings. This happens now on all versions & regardless of whether 'und' is included as a subtitle type (also, the subtitles did not appear).