FC's just pass on the electricity that you give them. Power is a direct connection like a wire among all the ESC/servo connections, MainPort, FlexiPort and the Rx power too. There are some current limits. You wouldn't want to run a 700 heli swash plate servo from it, but for normal servos and normal flight loads it shouldn't be a problem.
This usually happens because you forgot to program the transmitter to use that switch for that channel. Modern transmitters with all the channels and switches typically only default to the 4 stick channels being programmed by default.