Probably by now you've worked around your problem, but I wanted to post the solution for others who might hit this later.

Your issue is the Intel EHCI compliance test tool. If you disable it in Device Manager, I bet that your system will start recognizing USB after a reboot.

I had your problem this morning, and disabling the Intel EHCI compliance test tool worked for me.

I work for a company that makes USB devices. That Intel tool is a compliance test tool that manufacturers/testers use to make sure that their devices meet the USB spec. It's a known issue that the test disables your ports. End users get no benefits from this tool; just dead USB ports.