seems like I'm having the same issue (I just noticed today)
I have some mkv containers that worked after the libxine1 update and now they don't. I have verified the /etc/apt/preferences and sources.list and did the apt-get updates and upgrade, even dist-upgrade and everything seems to be up-to=date; yet some 1080p mkv containers work and some don't and some of the ones that don't work used to work after the libxine update of 2010-07-27 23202.
some will just freeze... at like 6 seconds into the video...
the log files say a bunch of stuff, but there doesn't seem to be a difference between a mkv that works and one that doesn't. so, the same mkv that used to play, no longer plays. It didn't play before the libxine1 update, then after the update it did ( a few months ago )
and today I noticed it doesn't anymore ( but it could have started a few weeks ago, I started investigating today). I haven't really done anything different; except maybe a update now and then when I started playing with asterisk and then again recently when I realized quite a few newly acquired mkv's were not working; thats when I went back today to test older containers that worked fine and turned out not be working.