USB 3.0 is sometimes flaky, I don't really understand why. They didn't exactly nail the backwards compatibility; I've had a surprising number of problems with it - enough that I have a USB 2.0 hub stuck to my monitor, which has a usb 3.0 hub built in... (no arduino specific problems that I can remember, but lots of devices just refuse to work in USB 3.0 ports, or work once and then stop - at least on my system)
Sticking a $3 (yup, they're that cheap now) usb 2.0 hub between the port and the device is enough to make it behave normally.