Hi again,
Maybe uninstall all drivers USB.
If you want, clean register base and other part of system  with CCleaner:
http://www.piriform.com/ccleanerIf you have the patience to look at the sites of the manufacturer drivers the most up to date, it would be better.
But if I am you,  I do not would install the USB3 drivers. Not immediately.
After the uninstallation, I would shut down the computer.
I plug something into the USB2 port to see if it works.
Note for BIOS: 
Have you set these parameters  Enabled or Disabled or Auto?
xHCI preboot 
xHCI mode 
HS port switchable 
xHCI stream
USB 2 controller
XHCI hand-off
EHCI hand-off 
onboard USB3 
Normaly this are Enabled ...and Auto for xHCI mode
Note :
 What is your windows version? 64 bit ultimate , Service Pack 1, ... ?
Come back here to give me news.