Hi Simon,
I have the GA-Z68UD3P-B3 mobo which uses the same Etron EJ168 USB3 Chips as your motherboard and I am running the latest Etron drivers which are 1.11 that I downloaded from here:
http://www.station-drivers.com/page/etron.htm these are working better on my system than previous drivers.
Also have you tried the latest BIOS for your motherboard which is F10, that you can download from TweakTown here:
http://forums.tweaktown.com/gigabyte/28441-gigabyte-latest-beta-bios.html as a recent update for my own board has also helped?
I would beg to differ with
DM over disabling the USB3 Turbo feature in BIOS as I have actually found that this can help but the transfer speeds of different devices does vary widely. For example, a SATA2 Seagate HDD attached via a USB3 dock gives very fast speeds on my system as does my ADATA 8GB USB3 Pendrive. But, a SATA2 Hitachi Deskstar and an un-named brand 32GB USB3 Pendrive I have perform very poorly in comparison.
So the other variable of USB3 hardware that you are using could well have an impact on performance rather than it being BIOS, Drivers or motherboard implementation and is worth bearing in mind when trying to find solutions.