I have an 06 with the same problem sometimes and I read in my manual to reset the windows you have to roll both windows down and back up 5 times. Here's the link on how to do it:
http://www.stangpit.com/wp-content/i...b/06-22-18.pdf If that doesn't work then you could also pull off the panel on the inside of your door that the button is on and make sure the wires are not pinched.