I recently bought a USB 3.0 hard drive enclosure so i could use it as my backups directory. I followed the instructions hooked everything up and double check that i had a USB 3.0 cable and i was using my 3.0 ports. Everything looked fine except when I opened up my disk partitioning manager the program said it was running at 480mbps which is USB 2.0 speed. I knew something was wrong so i checked to see the speed the kernel was registering.
Using the following command
I was returned with a list of 6 numbers usb1,2,3,5 read 480 while usb4,6 speed file read at 5000

So i knew the kernel saw the usb ports. and i checked else where using gnome-device-manager i found a listing of all my usb devices were under two ehci controllers one for usb1 and one for usb2 i found no mention of my xhci controllers or my two missing ehci controllers until i went under every device heading and my missing controllers were labeled under pci bridge instead of directly as there own root controller and i no matter what usb port i use i can not access my controllers.

Has anyone ever come across this sort of problem?

For some reason I believe the usb 3 is to the OS a single, separate chip. It doesn't follow the old dual chip idea of 2.0.

Try a few live cd's to see if they support your 3.0 chipset. It may be possible that this board has been made functionally as a chipset on a pci to pci bridge or other that needs to be working.

I assume too that bios enabled and no hardware conflicts exist.

Hmmm thinking I was getting a conflict error as the Bios was having issue handing off xHCI support to the kernel so I disabled having bios handle the xHCI so the kernel could pick it up.