Just in case you are still trying to figure this out...
I have the same motherboard on a new build and was having the same issues. After some digging around I discovered that 9.3 by default has USB 3.0 turned off (find 'xhci' @
http://doc.freenas.org/9.3/freenas_intro.html). I booted the system up using a 2.0 port, then added the suggested tunable (xhci_load: YES). After that, I was able to boot using a 3.0 port. I just moved my boot flash drive back onto the motherboard internal USB (which is 3.0) today and everything is working perfectly; power cycles are running as expected.
I was originally looking into this to help with the lack of USB 2.0 ports on this board. The motherboard only has 2 of them and with a keyboard, boot drive, and USB linked UPS I needed one more for convenience sake. In the bios there is also the ability to downgrade USB 3.0 to 2.0(in southbridge). I didn't have any luck with downgrading them though.
I'm running 9.3-current-201503130047. The USB drive is a Team C134 16GB.