The moral of the story: just because there is a new version of VLC does not mean "upgrading" to it is desirable. It used to be that to get a version of VLC which did anything useful, you had to use unstable, as nothing sufficiently cutting-edge was marked stable.
Now, a perfectly working version is stable, and unstable is so bleeding edge that it's broken; upgraded to 0.9.0_alpha20080110 as part of my usual automatic upgrading last week. They seem to have tweaked the UI in ways I'm not sure I like, but, worse, it doesn't seem to be able to play matroska files anymore. Gah. Hopefully downgrading will help, as I can't think of much else to try. I'm pretty sure it's that, and not some black magic involving having improved my video drivers.
On the Good News front, Arisia tomorrow!