Some how your windows lost their programing, in your owners manual (on pg. 46) there is the procedure on how to reprogram the Short Drop Feature. Shouldn't take more than a few minutes.
With the doors closed and the key on do the following:
1) Push and hold the window switch down until the window is full down and hold for 2 seconds more
2) Release switch and Immediately pull up and hold the switch until the window makes full up and hold another 2 seconds.
This should restore your auto up/down as well as the short drop.