of course like an ass I missed the whole second page of the thread. Since you know how to check voltages, try check them while the the connector is connected to the mobo, and also try when it's not connected. There maybe be more then just +5 and 12v on some of those pins. They are color coded. If you get something strange, let us know. Some computers have weird voltages, like -5 and -12v. Some components require negatives for reasons I can't recall.
Sometimes to check a pin while the p/s is connected to the mobo, you might need to utilize a paper clip or somehting, by shoving it down between the wire and the plastic of the connector. Be gentle and be careful not to short (connect to metallic points that were never meant to be). Common sense will be your guide.
If you're say reading 5vdc on a particular pin when it's not connected, but something different when it is, the problem could be the p/s. Or a short somewhere as been suggested. That would require a visual examination of the circuit board (got an eye loupe handy?). It usually doesn't take too much investingating to determine if the power is bad though. Usually.