It is theorized that the older systems only use one 4 pin CPU connector and the newer systems use two. The theory further hypothesizes that the power supply senses that the second four pin connector is not connected and as a result never sends the power-good signal causing the system not to boot even though power is available. The power supplies are made by lite on or Delta, I have a Delta model DPS-500AB-49 A.
Can you try to figure out the pinout of the second connector? Sounds like it's doing remote sense all the way to the motherboard.
Sure, There are only 5 connectors.
P1: 6 pin MB connector, 2x +12v, 2x G, PS-ON, PS-OK
P2: 4 pin CPU connector, 2x +12v, 2x G
P3: 8 pin GPU connextor, 3x +12v, 5x G
P4: 4 pin CPU connector, 2x +12v, 2x G (This would be what I call the "second" connector, though I tried with only this one connected as well and got the same results.)
P5: 6 pin GPU connector, 3x +12v, 3x G
And some pictures of the innards. +12VBDC (Purple wires) go exclusively to the MB 6 pin connector. +12VADC and +12VCDC (Brown wires) go to the CPU and GPU connectors but I didn't trace the exact split yet.