It was a bit strange but after the battery was replaced on my car, the auto-down on the window no longer worked. Luckily it's a known quirk and it's an easy fix.
You just need to reset the window control unit by:
- Winding it down all the way
- Winding it all the way back up
- When it reaches the top, keep holding up for another 3 seconds.
The window should now have auto-up/auto-down enabled again.