Have you removed the cooler backplate to verify it's not that which is shorting something on the back of the motherboard? Wouldn't be the first time that a Coolermaster backplate has made improper contact with components at the back of the board although am only familiar with it happening on some of their air coolers, and depending on the motherboard as well. Just something else to try.
No haven't tried that... remove the backplate and CPU? I tried running the mobo without the CPU in but couldn't get it to turn on at all. Thought mobos could fire up without a cpu attached?