Hooray thread revival!
Anyway, I found out that everything actually compiles like it should. But the kicker was that all the output was hidden, including the "press any key to continue" line. Fortunately there's an easy fix: run BSP in wine via the command line. The batch files will output there. It's a bit of a mess, but it works. Maybe I'll post some modded batch files a bit later to fix that...