Thank you for fixing the problem, although I'm not sure that non-FOF bases should be used here... Did you notice that there's a 25% gravity decrease that affects every sector? Per haps that's got something to do with the flag spawning, because even when I removed the reverse gravity on the Team Base sector, it still spawns on the floor.
EDIT: Well, that sucks. Even when I turn off all the gravity flippers in the sector, every single one, the flag still spawns on the bottom. It seems this map just isn't very good for CTF--I originally designed it for Match anyway. I guess I'll just keep it like that, since that enormous blue column sticking out from the bottom of the station was an enormous visual obstruction, and I certainly don't want to have two of those.