I'm not using the adapter that came with the board. The system is in a Cooler Master Storm Enforcer that came with 2 USB 2.0 and 2 USB 3.0 ports pre-mounted on the front with their own cable that connected to the USB 3.0 header on the board.
About the same time as I got the email notification of your post I had started to suspect that the problem is not with the mobo but with the cable or the ports. I haven't yet had a chance to take things apart, but that's where I'm going next.
I still have the USB 3.0 adapter that came with the board, so the easiest way to test things will be to connect that to the header. If those ports work when connected to the board, then I'll have narrowed things down quite a bit.