>> What do you mean any earthing going on? How would I be able to tell? The mobo stands are the riser screws right?
Correct. Mind couldn't find right words.
Remove motherboard from case and place on piece of cardboard. This will stop it touching the case. Reconnect power supply and power switch. See if problem still occurs.
If it does you've isolated the problem to either power supply or motherboard.
Oh, and silly question. The auxillary power supply cable is connected to motherboard isn't it?