@ThermalMike tried that mate, just killed everything. I got the random flashing that I saw mentioned in other threads. Tried all types of combinations of where to put the headers in relation to the fans, and even going back to where I started, every time I set the fans to PWM in bios, the LEDs start randomly flashing.
I have installed the original controller again and it works a tread so my guess is that this controller is faulty, or the MOBO doesnt like it. Which sucks as my OCD loved everything looking the same!