I truly understand your problem.

I have 2 cats that MUST be indoor-outdoor cats. One will pee on kitchen counters and yowl, the other will self-mutilate and bleed all over. They are allowed to use the doggy door (as are the 2 dogs) during the day. The other 10 are kept in their own room, with a large, totally enclosed pen accesible through a cat flap through their window. In the evenings, I let them all mingle throughout the house with the doggy door locked.

The only suggestion I can think of would be the cat flap that requires a special collar to open the flap. One is the PetSafe Infrared cat flap at $119 and comes with 2 collars. See the DrsFosterSmith.com site.