I have the same problem and same scenario.  After a power surge last week, only my 3.0 USB ports are dead.  I'm going to open up the box and check everything.  I post my tests, results and what I did to fix it - if I can. 

Hitman47222 what type of motherboard are you using?  I'm using a GIGABYTE  78LMT-USB3Update

I disabled/enabled my USB 3.0 controller in the BIOS and that didn't work
I tried to re-install the 3.0 drivers via windows and it said the hardware wasn't there

I removed the controller physically, powered up pc and then shut it down.  Put the controller back on and power up the PC and now it is recognized and works.  Here is another EXAMPLE of how removing it physically and putting it back on after a power loss/surge fixes USB 3.0.

very weird.
Hi

I think turning the computer off for a few minutes or if a laptop disconnecting the battery and power for a few minutes would have FIXED it. USB ports have THERMAL fuses that require power to be completely removed and a time for them to cool to reset.

A quote from WIKIPEDIA

When power is removed, the heating due to the holding current will stop and the PPTC device will cool. As the device cools, it regains its original crystalline structure and returns to a low resistance state where it can hold the current as specified for the device.

The full page is here http://en.wikipedia.org/wiki/Resettable_fuse Quote

USB ports have thermal fuses that require power to be completely removed and a time for them to cool to reset.

   Source that these are used for USB ports ? ?

Rick Hapanowicz

Positive-temperature-coefficient devices do the job and provide stand-alone compliance with IEC 950 and UL/CSA 1950.

With the surge in computer applications that incorporate plug-and-play or hot-swapping, designing for compliance with safety agency standards has BECOME more critical. A development worthy of examination in this regard is the universal serial bus, a specification many manufacturers are adopting in order to provide a uniform protocol for the addition and configuration of computer peripherals.
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