I am not from Intel and don't know whether it is this situation, but I'll mention just in case. It was mentioned in another thread that the USB driver installer asked user to reboot before it had fully finished installing, so that if you rebooted too quickly the driver ended up in some sort of limbo state. If so maybe you can try removing and re-installing the driver but wait longer this time before rebooting? Keyboard and mouse not working after USB3 driver install
Also are you using Windows 7 or something else? I use Windows 8.1 and never even noticed until your question that there was a USB 3.0 driver for download - I'm fairly certain that I've used devices at USB3 speeds without ever having installed Intel's USB3 driver.
Update: you may also want to let us known your BIOS version and what is your setting for xHCI mode in the Visual BIOS. Release notes for BIOS version 40 say they fixed a bug that was in version 38 regarding not defaulting to the Smart Auto setting for xHCI (I'm not sure what it was set to instead or whether that would matter for your particular situation).
Thanks for the thoughts. I had read about the delay in installing the USB3 driver. I don't believe this is the case anymore, but I waited an extra long time just in case. The pop-up window said that the USB3 Hub was ready before the Reboot option was available.
I talked to a friend at work who also indicated that this might be a BIOS issue.
I dug around and turned off Legacy USB mode. That seems to have fixed everything.
I appreciate you taking the time to help me with this problem.