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There is one more issue that could be the problem, there might be something shorting out the wires like metal from the case or a loose screw stuck between the mobo and case or a nick in the wires.

Don't know how I could have forgotten this one but It could also be that the case wires are shorted or shorting out on something metal in the case could be an extra screw that might be stuck between...

There are only two issues that could be at fault the motherboard or the incorrect placement of the power/case wires. If all else fails try the phone book and have the rig bench tested by a...