Just wanted to add to this thread in case it helps anyone:
I just did a build with the Z97-AR, nothing unusual. I7-4790, 2x8GB 1600, OCZ Vector 180 SSD, Windows 7. Installed all of the ASUS drivers from the included disk. All of my USB devices were showing as USB 2. After a BIOS update, same thing.
Called ASUS support, they directed me to new Intel USB3 drivers on the ASUS support page for the Z97-AR. Installed the drivers, reset the BIOS to default (per their recommendation), and then I had working USB 3 ports.