Not much progress on this. Tried a new rev 1.0 board and it displays the same problem, so it's either inherent on the board's design or a OS issue. There seem to be a few people around with similar problems with USB3 ports on various boards, so it's looking rather like the later, possibly related to the driver installation process.
Gigabyte are totally useless for technical support. The replies are so poor it's pathetic.
This reminds me of my 1366 board from Gigabyte, the UD7.. but is applicable to all their 1366 boards with the Marvel 9128 SATA III controller. To make it short, you only get so much speed from this combination and it's not the full rated SATA III speed. The controller caps at roughly 400mbps on reading and 275 writing.. There's enough settings, drivers, etc,, to keep a top notch technical support team like Gigabytes (please recognize this as sarcasm) asking you to jump through hoops for weeks or longer. Other than this issue it's been a reliable board.