Someone on the Z4 just reported the same issue. He used the key fob in the slot and cycled the car off and on a few times. The windows worked again.

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Richard
Sir Snaps-a-lot, 9 Time Dragon Slayer (54 runs!)
2011 X5 50i Alpine White, Biege Nappa /Lt Poplar M Sport
2009 Z4 35i, Black Sapphire/Ivory-Black/Anthracite

Gone but not forgotten: '08 550i, '06 X3, '06 650i, '02 M5, '99 540i