I think i do have the solution for you. As you can see, i was had this problem, and simple driver install took case of it!
But was it that simple. I found that if you head on to MSI's website, and find the drivers for download (for windows 7 64bit -
http://www.msi.com/product/mb/Z77-MPOWER.html#/?div=Driver&os=Win7 64)
The first on the list looks like a golden pick! Intel USB3.0 Driver, how could this not fail! It is failing if you have the same issue as me.
After many attempts, i took a closer look. As i looked down the list, the 4th choice in driver also talked about USB3.0, but why? The driver is above (granted its not working, but its there)
I downloaded the "Renesas USB 3.0 Driver (3.xx)" installed it, and off we went with a full set of working USB 3.0 ports!
Hope this helps, as you problems sounds identical to mine.
(I do know this ^^^^ does not reflect much on what i wrote above that a reinstall worked, it did work, but only cos i picked the other driver and didnt think much about it until days after)