Armorlight, there are many BIOS version that fixed issues related to USB 3.0.
According to your post, you already have the latest BIOS version installed. Do you know which BIOS were flash on your system before the latest one?
You may want to test your system out of the chassis, minimal configuration such as motherboard, processor, power supply, 1 memory stick.
You can also try removing the CMOS battery and leave the system without it for about an hour. Then put it back on and restart the system. http://www.intel.com/support/motherboards/desktop/sb/CS-028780.htm?wapkw=clear+cmos+battery#datetime
Which devices are being recognized on the working USB port?