I have the the same problem almost one year, but I know how to temporary resolve it and how to reproduce it.
I have new bios 2.10.
USB3.0 after some time will loose power only if I have turned on "OC Genie" option in bios.
USB3.0 will work with OC Genie ON only until my PC will loose power when its working (for example after unplug power cord, energy blackdown(not always))
If USB3.0 will loose power for me only helps OC Genie off, restart, OC Genie on. After this USB3.0 will work again for some time.
I think its bios problem because of OG Genie.
My English isn't perfect but i hope you can understand me