Its probably the least likely. Does the air blow hot all the time? If not then its likely they are working. Maybe the pipes are getting hot / cold, but not really hot / cold as they should be. You really need to know the evaporator temperature. Mind you, it doesn't always happen, does it? Maybe the flaps are sticking when its hot? There are separate temperature flaps for left and right, so if both sides aren't working they would have to be both faulty. Perhaps run the self test when its playing up:
atc-diagnostics-t5659.html