I have been playing around with USB3 on this NUC for a while now and the one thing that I have discovered is that if I disconnect my devices from ALL the USB3 ports and then let Win 8.1 64bit boot, I can then plug all the devices in when Windows is loaded and they all work fine.
I have also found that I cannot do a BIOS Recovery from the front ports, only the back ports.
I know this doesn't help but it does point to a booting problem of some kind.