Hello
rirussint, I see You have last BIOS package.
Have You try to remove any additional PCI-Express cards (like RAID controllers, Sound Blaster card etc.) form the system, than apply firmware update for USB 3.0 again
please be sure You run cmd line with Administrator rights when running firmware update for USB 3.0 and executing both (front and rear) firmware updates finish with no errors.
Next I recommend to go in to motherboard bios (F2 at startup) and load bios default settings, save and reboot motherboard than enter to verify if everything working correctly.
I assume for Windows 8 there is no driver package for USB 3.0, so please be sure You download and install all necessary updates from Microsoft (using Windows Update).
Please be sure You have installed Intel chipset inf. Drivers : https://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=20462&lang=eng
and management engine drivers :
https://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=22090&lang=eng
(after that OS reboot may be necessary).
I am using Windows 7 x64 Ultimate and after USB 3.0 firmware update with BIOS 0559 I have no problems with USB 3.0 ports (front and rear) for the past month.
I also made test on Windows 8 when I troubleshooting this issue, I simply put new HDD, install Win 8 x64 Prof, install all drivers from Intel + Nvidia SVGA driver, than I apply all Windows update fixes and do test on rear USB 3.0 ports – it works grate for about 4 hours.
It was no problems, even when I reboot OS for few times, power it off and then on (with power cord unplugging), adding additional PCI-Express card (first SB Recon3D than RAID controller card) and so on.
After that I switch back HDD for my Win 7 OS (with I use for work, games and internet browsing) and never again get back to Win 8 on this platform.
I hope I help You with troubleshooting Your problem and resolving it.
Best Regards
Piotr