Cinema display USB stops working after upgrading to mountain lion

I am using a newly bought 27' Cinema display + mid 2011 MBA. an Apple USB keyboard is attached to the display USB port, and a logitech mouse is attached to the USB port on the keyboard.
After upgrading to mountain lion, when I unplug the thunderbolt from MBA, and then plug it back, the USB keyboard and mouse stops working. Moreover, I cannot open anything in System preference, and cannot properly shutdown the machine!
Please help on this issue.

Launch Terminal, type or copy/paste the following:
killall Dock
Hit enter.

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