I know this might sound like the obvious and u probz might think that im callin u newbie mapper but have u run the BSP in the compile options?
If u have then the only solution i can think of is that ur .VMF file isn't in the same directory as ur .BSP i encountered problems when i was sending my .VMF back and forth over a network without the .BSP and compiled it once on each computer. This seriously screwed up my map and it kept reverting to the old .BSP without making a new one. I'm not much of an expert when it comes to understanding code issues, thats all i can think of dude.