You said you have slow usb speeds via thumb drive? How do you know its the MoBo? I'm geussing you tested the thumb drive on another computer as well as a different usb drive, and different usb ports.
Sounds like the usb is running at the old 1.x specs, and would account for the low speeds. If you really did cook that function off your mobo then the only fix I could suggest would be to buy a pci usb card if you really use usb alot. Replacing the motherboard is too much cost, time, and effort if thats the only complaint with it.
Ok some things to check out here, first off check to see if you have a driver conflict in the device manager(Goto start > run > type 'devmgmt.msc') USB stuff is at the bottem. Expand the USB info at the bottem and tell me what the first 2 lines are in that list. Lastly search MSIs web site for new usb drivers, install them and prey.