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This is shit. If you had plugged in an USB 2.0 device before plugging in the USB 3 disk, the port may stay in USB 2 mode.
How do I get the best performance from the USB 3 ports?
The first device you plug in will configure the port, so always connect USB 3 capable hubs or devices first.
http://support.apple.com/kb/HT5172?viewlocale=en_US#8
The only solution is to reboot the system. Happy, my disk is not broken, unhappy because this is shit.