usb 3 driver updates sometimes require a BIOS update to support them. If windows detects that the USB drivers are messing up, it could have updated your generic USB 3 drivers and then they would not work because it can not update the BIOS for your.
(generally bios versions after about march of 2013 work correctly for usb 3.0, not sure of the date for usb 3.1)
so check for a BIOS update for your motherboard vendor website for a BIOS update and for any USB 3.0 driver updates.
there are also some conditions that will cause usb ports to be shutdown. (too much current being used, mostly because of apple products that violate the rules on how much current to use. Custom driver will allow the violation but if they got updated by windows...