I just had to reinstall windows and as Shaun suggested, the USB 3.0 was not recognized. Use 2.0. This may also be true for your keyboard and mouse.
Also, when installing windows, when you get to the first selection screen, the installer may say that it cant find the media. If so, click cancel and get back to the Install Windows button, then remove the USB and try another USB 2.0 port and try again. I had to repeat this 4 or 5 times for it to work.