I found this out yesterday...
When raising my top, I wanted my windows down after the top was up. So as the top was going up, I pressed my window button down till it clicked into the auto down mode. (you know, you can press your window button farther than normal and let go and the window will continue to lower by itself)
After the top was up and the windows raised to close as normal...the windows then lowered again.
SLKman