Well, if there is space between the top of the case and the power supply then the air flow should still be fine, same as otherwise, it just wouldn't suck up any hot air from the case. I had this issue with a power supply once, and it was ok. Well the controller just changes the voltages going to each fan, and order they are plugged in shouldn't really matter that would just be for convenience. Hmm, so it would seem that there is a voltage issue, or that the switches don't work on the dials. Have you looked around to see if this is common?