Don't worry, you haven't done anythiong wrong. Removing the Negative terminal is a soft reset for the system, same as you have to reset your radio settings you have to reset your power windows.
1. With the car on, push the windows Down button to activate the windows, then hold it down for 3 more seconds. Release.
2. Pull the windows Up button to activate the windows, hold it up for 3 seconds. Release.
3. Push the windows down button and release, the windows should go all the way down on their own.
4. Pull the windows up button and release, the windows should go all the way up on their own.
