This might be a very dumb question, but are you sure you are using a USB 3 cable?
Just a thought because a friend of mine thought he could just use a standard USB 2 cable and of course he could but did not get any 3.0 speeds.
Also, not all USB 3.0 cables are the same. I have 2 that don't work very well at all and others that do just fine.
Have you tried a USB 3.0 flash drive in the ports?