Have you tried unplugging all drives except for the windows based drive and having it plugged into the original sata port?
Yes, I am currently running the rig with just the ssd boot drive. No problems.
I can't remember which drives were plugged into which SATA ports. When installing the new PSU, I decided to replace some long SATA cables with short ones. I thought SATA ports were like usb ports - ie if they're the same speed, they're interchangeable. Maybe I'm wrong about that as well. haha