The first thing to do before reinstalling Windows or doing anything else would have been to even borrow a known working supply to see find the new supply as the cause or to see that ruled out. By using a substitute and seeing the system run normal you would simply return a bad supply to the vendor for an exchange, substitute, or refund.
Sometimes supplies will see loose contacts inside one of the power connectors either the main 20+4pin or the 12v cpu feed. Since you already swapped boards out it's most likely an internal problem with the supply itself. The thing to do now is swap the current supply with another to see if the problem is corrected.
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