sounds to me like you have a problem with your sensor -- the one located just above your rear-view mirror. It senses whether the top is fully closed or not and will not allow you to fully roll up your windows if it does not think the top is closed.
my bet is that this sensor is bad or perhaps just stuck in some way (when the top locks down, the sensor actually 'clicks' in). you should be able to push it with your finger and hear the clicking.
good luck.