I just wanted to say thanks to all the folks who mailed me and offered advice about different things I could try. Some people pointed out that I hadn't tried TXQbsp, which comes with quark, but unfortuanely that doesn't quite work either (problems seem the same as those with WQbsp). Right now I'm having a look at the Qbsp source myself to see if there's anything I can do there. Time will tell...