You probably have a VBSP error that is popping up, like an Invalid solid or a displacement thats an entity.
Hit alt+p and that'll tell you if you have any issues with your solids.
everything else? just copy the compile log into here. It'll check everything for you and tell you anything that might be wrong. If that still doesn't help, bug us again (or bug us if you questions!)
Then you have a bsp error. I assume when you checked for leaks you compiled the map, went to load the maps point file, then recompiled and checked again? Once you plug a leak you have to recompile before you check for another leak.
Also, might you accidently have 2 sky cameras, one being in the ground in the main map? Check the entity report to be sure.
This might all sound really silly, I just want to make sure to cover all the bases, since I don't know what you do and don't know.
I did the entity report, and turns out there was a sky_camera under Red's base for no reason. Thanks!