"an areaportal must shut off an area and can't be reached by more then 2 sides"
Ahh, that was my problem, I did not know that limit of the q3 engine. I made a quick caulk brush to cover one way into the base and reduce the number of sides down to 2 and everything worked fine. I will have to tweak my layout to fix this but I have all ready thought of a few things I could do. Thanks for the help SS. :D
I put the new in b.