Ok, so you have power running to the inbuilt fan controller and then the TOP and REAR Fan are connected to the Fan controller on separate switches - so you are saying the Fan Controller is not getting any power at all?
Is the Power socket to the Fan controller still connected to the PSU? The TOP and REAR fan should be connected to the controller via the little 2 pin connectors that look like these http://puu.sh/aiQTv/6606d225cd.jpg, the controller itself needs to be powered by this connector
http://puu.sh/aiQUm/613b71a5f3.jpg - make sure it's still plugged in to a Molex from the PSU.
Try by-passing the Fan controller and see if they come on - i.e. connect them with a Molex directly to the PSU or onto one of the extra Fan Headers on the MOBO if they reach.
Personally I don't muck around with Fan Controllers anymore - they're more hassle then they're worth. I just install PWM fans and run software to control them automatically depending on detected temps. It's much, much simpler that way. For instance, if you manually control your fans, if you have them low, you won't know your cooking until your already hot. The adverse is, if you run them at medium to high, it makes everything too noisy unnecessarily.