I know I have seen a post on the windows automatically going up and down when you open the door.

My Mini S quit doing that after I replaced a dead battery.

How do I get it to go back to normal?

 

With car turned on, open the door, hold the window up switch for a few seconds. You should see the window do its "up/down dance" at the top (immediately if the window was already up, or once it reaches the top).

Repeat for both windows. The shut / open the doors to verify.

With the door closed, you can also reset by holding the switch up for at least ten seconds. But door open reset is easier.