I experienced something kinda similar before
When I also thought the maps weren't compiling, but it was something with MBuilder

I have two installs of the game, "A" and "B"
In MBuilder I have set the "Game directory" path to the A install

But if I run the mohaa.exe from the B install, the next time I run MBuilder it will automatically change the game directory path to the B install, without any warning
And if I complile a map, it will copy the bsp to the wrong install

So after learning that, I always check the MBuilder paths before compiling, lol