I had a similar issue when I put all my gear into this case recently. Re-wired things (as I was an idiot and un-wired everything in the beginning) and magically I got all my fans working, and the controller (plus lights). Make sure that you have the molex connector connected in the back of the controller up in the top front corner. I think what did it for me is I tried a different power slot on the psu and things just worked. So yeah try to re-connect and make sure all the power connectors are good.