I'm having an almost identical problem with a Quadro controller. If I plug in the 5v molex to the PSU, with USB connected to a MB header, it won't power on. If I remove the 5v Power, it boots fine. It previously worked fine. I've tried two different power supplies (same problem), I've tried multiple different cables between the Quadro and the PSU, different ports on both PSUs, and different USB headers. The only thing I can't change easily is the Quadro.
Did you ever figure your problem out?