The issue has been resolved (well technically it was not even an issue to begin with >_<). I connected the hyper 212 fan to a sys_fan header and the fan spinned fine so there was nothing wrong with the fan. I then decided to connect the fan back to the cpu_fan header and just let it boot. After about 15 seconds the fan started to spin which must mean that the mobo sends outs a small amount of power which wasn't enough for the hyper 212 fan to spin but enough for the intel stock heatsink fan. But once the mobo detected that the cpu was started to get hot it sent more power through the cpu_fan header.
A member at Toms Hardware helped me out, he said some mobos do this (
Thread Link), but I wasn't aware of this feature or whatever you want to call it. Anyways thanks for the help.