Here is the FIX and no-one at Intel could point me towards it, very dissapointing ;
USB 3.0: Renesas Electronics* USB 3.0 Firmware Updates - Version:4.0.2.1; 2.0.2.0
This download record provides firmware updates for the back panel and front panel USB 3.0 ports (blue connectors) on the Intel® Desktop Boards DX79SR and DX79TO. These firmware updates resolve the following issues related to the USB 3.0 ports on these boards:
* BIOS and operating system do not detect devices attached to the USB 3.0 ports.<- This was my issue and it is now rectified.
* System hangs on POST code 58 for one minute if any device is attached to USB 3.0 ports, and then continues the boot process.
* In Device Manager, the Renesas* USB 3.0 eXtensible Host Controller is shown with a yellow bang and the error message "Windows has stopped this device because it has reported problems. Code 43".