@lostless thankyou. This has been driving me crazy but you hit the nail on the head. I had a driver installed for a case that had the option for cooling that must have used those pins. I uninstalled the driver and it is working now.
In my arcade build i found the fan that came with the flat pack kit was really loud when run from full power. It was a 12v fan. So i just found a left over 5v power brick and connected that to the fan and it runs about half speed, just the perfect amount of air flow without the noise.