rollbar stuck up and top wont go up or down

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battery went dead I syncronized they window work the first time every thing was fine till my wife left the lights and the new battery went dead again now the windows drop just a tiny bit as you open the door. like they are supposed too but the rollbar and top I can get to work again. I did not jump start the car I put a charger on it for about an hour. any ideas how the fix it.. thanks for any suggestions