I just recently upgraded my PC from Windows 7 to Windows 10 and I've been pretty happy so far. The only thing that's bugging me is my USB 3.0 ports. As the title says, on a cold boot, my USB 3.0 ports are clearly running at 2.0 speeds... I can't manage to get over ~35MB/s when I do a CrystalDiskMark test on my USB 3.0 drives (which I know are capable of far higher speeds). If I reboot the system, the USB 3.0 driver seems to load and I get the appropriate speeds.
I believe the drivers installed are the Microsoft ones. In Device Manager it says Intel(R) USB 3.0 eXtensible Host Controller - 1.0 (Microsoft), driver dated 3/28/16. And yes, that device/driver is always there in Device Manager, even when I'm clearly getting USB 2.0 speeds. There's no Windows 10 USB 3.0 driver for this board on either the Gigabyte or Intel websites.
I have another HTPC using the same USB 3.0 host controller driver, same Windows 10, but it's a ASUS board and it doesn't appear to have the same issues.
When I was running Windows 7 before, I didn't have this issue with the USB 3.0 ports. I did, however, recently update the BIOS to the latest (stable) F13 because I was having issues with failed posts. The F13 BIOS did in fact fix my failed posts, but I don't remember if I checked the USB 3.0 ports after the BIOS update while I was still running Windows 7.
So I dunno if this is a driver issue, or a BIOS issue. But FWIW, I did load optimized defaults.