I think i hve found the problem with .mkv's never playing to the end!!
in a post a guy says that if he quits the tsmuxer manually on mac osx using activity monitor it plays till the end. that is correct
i watch few .mkvs together (tv shows) and have noticed if after watching 2-3 if i check activity moniter i have multiple instances of both tsmuxer and also mencoder i think if you got them to quit after there is no more info to pass to the buffer that would fix the problem. becasue at teh minute i do not think they are quitting at all