You may need to 'reset' the window system. This can happen if the battery is disconnected and/or run-down (like on a left-over 2003
).
From inside the truck, roll the window all the way up. Then roll it half-way down. The roll it all the way up again and hold the up button for a few more seconds. I never noticed the wiper and heater issue but I did have a problem where the window button on the remote and the keyfob in the back didn't work. This procedure cleared that up and might work in your case too.