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Since you already preformed all the require troubleshooting, please try one more thing before replacing the motherboard.
Please proceed to test the motherboard with minimal configuration but out of the chassis to discard any grounding issue. (Motherboard, processor, power supply)
If you continue having the same behavior, feel free to contact your local Intel support group for assistance on replacing your product if it is still under warranty: http://www.intel.com/p/en_US/support/contactsupport?group=process
Thanks for the suggestion Silvia, I've just done the test you suggested and no change I'm afraid.
The board is on it's way back to Intel for replacement later today, I logged a warranty claim yesterday via the support line. To Intel's credit, the chap on the support line clearly knew what I he was talking about and he made the experience quite painless as I talked him through all that I had done so far.
Thanks again for your suggestion, that was definitely something I had overlooked.