You need to "reset" the controls. Do this to one window at a time.
1. Open the window.
2. Hold the button up to close the window, until it closes all the way, then continue to hold for 3-5 seconds. Then let go.
3. Hold the button down to open the window, until it is all the way open, and continue to hold for 3-5 seconds after it is open.
4. Repeat on other window.
5. use auto up/down feature again.