Before anybody asks: yes, I did try to re-calibrate, I did disconnect and reconnect the battery, I did reflash the computer, I did call the dealer, in fact I tried everything that's been discussed and suggested before on this forum.

Something new (and extremely annoying) has happened today: I got into the car this morning and when I closed the door, the window didn't bounce back up. I tried raising it completely with both the door closed and open, nothing. It wouldn't go any higher than the "short drop" position.
Next, I tried the re-calibration procedure from the owners' manual, but in order to to that, I should have been able to fully raise the window by pulling the switch up. My window no longer does that.
I parked the car when I got to the office and when I got off work 8 hrs later the window was still 1/2" lower than it should have been, the door was closed and locked, but the interior lights were on as if the door was open. The instrument panel display also read "Security event occured" and "Driver door ajar".
WTF, I don't get it anymore! Can anyone please explain and give a (new) suggestion?

Thanks!

I would have to think it is not neccasarilly a problem with the window, but a sensor for the door closing. Even though your door is closed, your windows are down. That tells me that it thinks your door is still open. You then set the alarm with the "door open". I think that is what caused a "security event occured".

Have the dealer look into your door latch.

Could also be in the GEM module that Ford uses to control stuff like this.

Let us know what they find out.