I have a bunch of MKVs with subtitles and playing any of them causes Boxee to instantly crash to Finder. I did some searching around the forums and discovered that there was an issue on the Windows side with MKV files using SSA subtitles. I stripped all the subs out of the MKVs using mkvtoolnix and now they play fine.
I just wanted to make people aware that this still appears to be an issue, at least on the Mac side.
I'm on one of the new Mac Minis (Snow Leopard, 2.4 GHz Core 2 Duo, 2GB RAM, GeForce 320M) and I'm running the latest Boxee downloaded from the main site.