This may not be your problem!
But there seem to be a problem my Intel Mobo's related to USB 3.0 too. I have a DZ68BC Mobo and I have no USB 3.0 devices connected to it and I have many Event Viewer ID 56 errors. These showed up from day one of my build. I have reported it to Intel today. You may have the same problems.
In researching this it seems to have something to do with the Renesas Electronics Driver,
The error say... Driver PCI returned an invalid ID for a child device (FFFFFFFFFFFFFFFF00)
See if you have this software go to Start>Renesas Electronics>USB 3.0 Host Controller Driver>3.0 Host Controller Utility, them right click on properties. Now click on the Security Tab then see if you have some Accounts Unknown followed by a long number in the User/Group window.
Hope you find your answer soon.