Wow, I wonder if that still is a thing?
I have never been more stumped and ended up reformatting (which I had been wanting to do anyways to move to a 1TB ssd)
The fix for it was pretty awful, as well. Under "System Devices", I'd locate the parts of the chipset associated with USB and PCI, find the driver the OS was referencing and remove the files associated with that driver from wherever in the OS they were being grabbed[1]. Then I'd download the chipset drivers from the chipset (not motherboard) manufacturer and install those. The problem always went away after that step, but often took several reboots to get everything exactly right for the new drivers.
It seemed to happen most commonly in Windows XP with motherboards that were Intel based and had USB 2 controllers with third-party (I want to say Realtek[2]) USB 3 controllers. At the time, Intel had no chipset that included a USB 3 controller so motherboard manufacturers would use a non-Intel controller for the USB 3 ports and the Intel controller for the USB 2 ports.
It's possible my problems were simply an artifact of working with USB 3 devices that were bleeding edge and not implemented exactly right, but in all cases replacing the chipset drivers with the ones provided by the chipset folks did the trick. Doing the same with the ones provided by the motherboard manufacturer (often ASUS for me) would result in the same behavior.
[1] The best way to do this, I've found, is to remove the files associated with the broken drivers and reboot. Once they came up as "Unknown Devices", I'd proceed with the installation of the drivers I grabbed from Intel/Whomever. If the device was detected properly -- in the case of this specific problem -- the new driver would be skipped in favor of the one provided by the motherboard or the Windows installation.
[2] I may not have this right. I tend to jump to Realtek when I think about devices I've had terrible experiences with. Their network adapters that seem to be included on a lot of lower quality motherboards have given me so many problems that I no longer purchase boards with them installed and if I have no other choice, I'll buy an Ethernet adapter from someone else and use up one of my PCIx slots just to avoid their drivers.