My USB 3.0 ports work, but not at USB 3.0 speeds, but this was the same in W7 and W8. I've given up on getting them to work at USB 3.0 speeds.
Do you know what make/model motherboard you have and do you know what USB 3.0 chipset you have i.e. Asmedia, NEC/Renesas or Intel? Windows installs the Intel USB 3.0 eXtensible Host Controller by default, but this driver may not work with your ports.
Knowing which chipset you have may help in providing a solution. Oh, did the USB 3.0 ports work before you upgraded to 8.1 and if so, at what speed?
Cliff