I would try this from the Intel download site after installing the USB 3.0 drivers if you haven't already...
After installing this USB 3.0 driver, your USB keyboard and mouse may not work in Windows*. This is only a driver installation related problem and is currently under investigation. Follow these steps to solve this problem:
1. During boot, press F8 to access the Advanced Boot Options menu.
2. Select "Last Known Good Configuration (advanced)".
The USB keyboard and mouse should now work in Windows.
So, I registered to post this in the hopes I could help someone else. I got it working but it's totally an intel programmer snafu with the installer. When you're done installing the usb 3 driver from intel it will ask you to restart your computer. DO NOT RESTART. The driver isn;t actually done installing according to windows. You need to wait for windows to announce via a system tray popup that the intel usb 3.0 root hub is finished installing. The installer will force reboot the machine in the middle of this process and leave the driver in a partially installed limbo state. I was able to fix it by re-installing the same driver over again once I booted to safe mode once and then rebooted again (the usual last known good configuration method) a few times. Now it reboots just fine and all my USB ports work. Hope this helps.
I had the same problem. I had Windows 7 loaded and running, updated the Intel USB 3.0 driver, and poof, keyboard and mouse no longer worked even in the BIOS. I was using logitech wireless keyboard and mouse. Intel support had me switch to wired keyboard and mouse. I was then able to get into BIOS and hit F9 to reset to factory defaults. Wired keyboard and mouse now work in Windows.
What a pain
Thank you for the information you have shared with us kittani.
rjb48356 we apologize for any inconvenience this has caused to you and as Nixiedesk mentioned on the previous information he posted, this is only a driver installation related problem and is currently under investigation.
You can see the information here:
Thanks and regards!