Man, fontconfig is probably one of the most annoying things I've ever used.
You guys may or may not want to try Perian 1.0, which may or may not add near-complete MKV support to Quicktime, with a subtitle renderer that I may or may not have written!
http://www.perian.org/
Subtitle rendering problems are probably bugs in Quartz/ATSUI, but you can tell me about them anyway. Some files (ex: [sudo]) have slightly-broken fonts, and some (Triad StrikerS) mp4 files have broken audio, but mplayer objects to them too, so I think it's their fault.