that my friend is a very bad and annoying bug that is very difficult to get rid of in SP. We’ve posted some extensive info on this bug over at KoS’s place (SP specific mapping), have a look in this thread
http://kos.spot.com.au/forum/viewtopic.php?t=200
In the mean time try using the -nocollapse switch during (light?? - can’t remember which section it’s in) compile.
The problem though is this… if that doesn’t get rid of the problem you’re stuck, we’ve all had exactly the same problem and unfortunalty as a result all the SP’ers have switched back to q3map. You can waste a lot of time trying to get q3map2 to work with this, it currently won’t (or at least we haven’t figuered out what’s causing it or how to fix it…! Just speculative guessing at the moment as it’s more then a simple shader overflow which Fiesling mentioned which is easy to fix).
We’ve been figuring that there’s some odd limit/combination of settings/circumstances that make this bug appear which don’t appear to effect MP mapping as bad…