Um, I think you had a dead battery and now all the windows (& sunroof) need to relearn the auto-up anti-pinch feature. Roll the windows up manually - don't push the window button through the "click" into the auto up feature. When all the way up, push through the click and hold for 2-3 seconds. The window learns where it is all the way closed, so it can tell the difference between being closed and pinching your kids fingers.
I don't think there's anything wrong with your car, other than reaching the normal five life of the OEM battery.