I have a 2013 Cooper R56, and recently we had to jump start the battery, which was quite dead. The battery seems fine now, but co-incedentally, ever since then, the windows no longer return to their closed position when the doors are closed. Specifically, if you have the window up, then open the door, it automatically goes down a little bit, presumably to make a better seal on closing. However, if we then close the door, it now stays in its slightly lowered position. Repeated open/close cycles cause the window to become lower and lower.

Any suggestions how to address this?

 

I had this happen during a rainy spell here in Florida. It was so frustrating. I ended up taking the door panels off and probing the two larger wires with 12 volts from a smaller motorcycle battery to get the windows up. Then I left the windows unplugged until I could figure it out. All research led to the FRM footwell board behind the drivers side kick panel. Apparently low battery voltage wipes out the e prom. Tons of reprogramming sources on eBay. I'm waiting on mine now.

 

Footwell module returned from programmer. They found nothing wrong. "Sigh"