Ok.. So I FINALLY found what the problem was and made a working work around. It turns out that the original power supply had an extra 3 wire plug on it for the motherboard. My best guess is this cable sent a pulse to the motherboard telling it it has power and can do stuff. The new power supply only has the 2 wire switch for power. So.. I wired in a master power switch to those wires and converted the factory switch into a start/reset switch... so now it functions more or less like a much older system. I can get it to post consistently now... just takes an extra step.