The cc3d doesn't do anything with the power, it just passes it from whatever port you plug the 5 volts into over to the other ports on the board.
Some people think plugging in USB will power other things plugged into the cc3d, it doesn't, USB only powers the cc3d itself. Everything else has to be powered by a battery the same as when it's in flight.
If that's not your problem please post more info or pictures of how everything is wired.