That's odd, but I know I have had something similar with a Fury stick, it doesn't show up, but is still recognized by e.g. Bfgminer.
Try to download
USBDview:
http://www.nirsoft.net/utils/usb_devices_view.htmlIt shows all devices, even "hidden" ones and if active or not, etc. You can easily delete drivers there. Might help to restart the install process.
I will check it out, but interestingly enough, I installed a VirtualBox VM running Windows 8 on this machine and then attached the two U1's to the VM's USB and now both of them work in the VM. I'm wondering if it has something to do with the Intel USB drivers for my Asus Maximus VI Hero motherboard.
EDIT:
Turns out that they are now working on my machine without running them in the VM. I uninstalled the drivers for the USB 3.0 controller on my motherboard and the cgminer version on the antminer github picks them up now. Of course, this means now my USB 3.0 ports don't work on my motherboard, so hopefully the cgminer/bfgminer devs will add support for multiple USB controllers in the future.