Driver side window doing strange things.

Sounds to me like maybe you need an exorcist.

I truly have no idea whether or not it can be programmed, but I seriously doubt it. That would make no sense. A bad power window switch is all that comes to mind, but even that makes no sense. I see a really weird grounding issue in your future, but the only reason I say that is that whenever I've come across a car problem that is so weird and random that it seems like I need an exorcist it turns out to be an intermittently bad ground. I can't tell you, however, how such a thing would cause this to happen

 

If it works the same way as a Gen 2, you wind the window down to halfway, then wind it back up except when it reaches the closed position hold the window button in the "up" position for an additional 3 - 5 seconds. That should retrain the auto open/close to the new closed position.

If the auto up/down was working fine, but this happens only when locking the car, then yeah, that is weird.

 

The Gen 1 had a feature where you could roll the window up or down by inserting the key, turning, and holding. Is there any chance that was what you were doing? "It's not a short, it's a feature!"

The disappearance of that feature was one of the ways you could tell if you had replaced your door lock actuator with a bum aftermarket one.

 

If it doesn't, you have a bum aftermarket actuator. If it does, you just have an aftermarket actuator.