I have a megane 1.5dci and i also have just put a new battery on and i had to reprogramme all the windows as follows, press down drivers window my went down in stages, when down hold button down for at least ten seconds then pull switch up untill window is shut and again hold for at least ten seconds, repeat on all four windows and it should be back to normal, i would imagine they are the same if not similar to yours, you can try it anyway you have nothing to loose, Good Luck.
WAKEY GEORGE.
August 2012