In order to get the map to consistantly compile to a BSP you have to save the map project in your "gamedata\base\maps" directory. I learned this the hard way after several bouts of trial and error. However, occasionaly you may have to resave the map under a different name. After several revisions of my map, the compiling process wouldnt overwrite the bsp to reflect my changes anymore. So by saving under a different name, it would compile a new bsp with my most recent version.
Im just a guy with a lightsaber and a few questions. ....Oh wait, I dont have a lightsaber. Uhhh...I dont really have any questions either. Ya know I think I'm in the wrong cantina too. Oh well, give me a shot of blue milk.