So we've left with this scenario: Front panel usb ports are connected to the mobo directly thru usb2 and usb 3 headers. This could now be the mobo itself, the cables connecting the ports to the mobo. As BIOS resetting/updating did not work it out. There is less we can do for the mobo. Try to unplug the header cables and then plug them again.
You may also be contacting mobo manufacturer for your complaint.