I had this problem on my 2006 2.0i. After changing the battery, on operating the roof to open both windows went down but after opening only the passengers window closed. On closing the roof the same thing happened. On searching the forum I found The Official Window Reset Procedure. http://www.zpost.com/forums/showthread.php?t=62834 I had to use this procedure a number of times until eventually the system worked properly. What I found was most importanwas to ensure that the one-touch operation of the window was erased both in up and down operation. This took a few goes to do it. Once the one-touch initialisation was erased, then go onto the next phase to program the window to operate properly. It does work but you have to persevere.
However I'm very pleased as it doesn't have to go to the garage for an expensive fix. Well done Forum, you've saved me a fortune in time and money.