I stumbled on this website a few days ago after having gone through the same pain on 3 different machines. 2 win8 laptops (x86 Panasonic with USB3 and Acer x64 with USB2) and an ASUS AMD chipset equipped UEFI desktop with USB3 running 2012 R2.
For the laptops the only solution was to reinstall after everything else I tried failed. I finally upgraded them to 8.1 and since then problem did not resurface (touch wood)
Reluctant to reinstall my server just for that, I keep digging deeper. Various BIOS settings did not change a thing.
I found finally a solution after I checked something that was not covered in the cool analysis on
http://janaxelson.com/usb_debug.htmThe windows system event log indicated each time an error from Kernel-PnP
"The driver \Driver\usblowerfilter failed to load for the device USB\VID_...etc"
All I had to do after I googled for it, and similar to this issue I knew of,
https://www.lumension.com/kb/Home/Endpoint-Security/The-video-and-or-HID-is-corrupted-after-Sanctuary-.aspxwas deleting the lowerfilter entry which had this "usblowerfilter" in:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Class\{36fc9e60-c465-11cf-8056-444553540000}
(and for safety I deleted them in the other controlsets too)
Since then the issue NEVER reappeared! Touching wood again tho!