Try turning off power management for ALL the USB Root Hubs in the Device Manager:
I.E. In Device Manager>USB root hub properties>Power management> untick the box that "allows the computer to turn off this device to save power"
I've found that with certain mobos, Windows has a habit of switching off USB ports to save power, whether or not anything is connected to them! This makes it seem like the keyboard/mouse or system has frozen up