Hey FGCOX1,
http://bradbarnett.net/mustangs/timeline/05/06/ownersmanual.pdf
The above link is to a pdf of the owner's manual. I actually was just avoiding work yesterday and read through this and it mentions your problem. Flip through a few pages and you'll find it but basically you continue to hold the window button in either the up or down position for 2 solid seconds after it's fully raised or lowered and it resets the system. It's basically just recalibrating the system. Hopefully that helps...
http://bradbarnett.net/mustangs/timeline/05/06/ownersmanual.pdf
The above link is to a pdf of the owner's manual. I actually was just avoiding work yesterday and read through this and it mentions your problem. Flip through a few pages and you'll find it but basically you continue to hold the window button in either the up or down position for 2 solid seconds after it's fully raised or lowered and it resets the system. It's basically just recalibrating the system. Hopefully that helps...