if you can flip the board over while it's running you'll see the pins for the PCI-E. one of the rows is +12v and tthe other is ground. Check those while it's trying to power up. It might be difficult to spot so watch the voltage carefully while you start cgminer.
Thanks again joeltang.
Just done that, while cgminer is running, flipped the board and used the check the voltage.. ALL 12.7v, no changes in volts.
When the cooler, fans are powering down and coming back on, is that the board resetting? (the 8 led strip cycles too)
Could it be a cooling issues? Seems strange to trigger it only milliseconds after starting cgminer (hasnt even logged into the pool yet to do anything). It only happens when starting cgminer.