Try the reset procedure located in your owners manual.
Get in the car, close door and turn ignition on.
Run window down manually all the way and hold the switch for 2-5 seconds.
Run the window all the way up and hold the switch up for 2-5 seconds.
Your window operation should be re "flashed" to work normally.
2013 GT Premium, Red Candy Metallic, Brembos, Auto, GT500 Axlebacks.
SOLD! 2008 GT Premium, Vapor Metallic, 5-speed stick w/MGW, Ford Racing M6066 Whipple S/C, 3.31 gear, GTA's. GT500 front end, spoiler, suspension and wheels. Sequentials and one touch. - can't wipe the smile off my face.