I just took a quick look. I didn't notice anything obvious, but the level flags were ambiguous on the brush (boxes rather than checks) and an ambiguous nodraw flag set. I made the level flags unambiguous, made sure no nodraw flags were set on any surfaces and gave all appropriate surfaces the nodraw texture instead. Not sure if any of this will really make a difference, but it was all I saw to explain the problem.
MCR, whenever you get a chance to download the new version I just committed (r29255), try compiling the map and see if it still happens. Compiling such a map can take more than an hour on my machine and I can't load up for a test just now.
