After putting in a new motor in the drivers door I still have the previous problem. When I use the keyless entry to remotely lock the car when all the windows are down it is still leaving the two front windows short of the top by around 6 inches, press remote again to unlock then again to lock for second time and they continue all the way up.

Any ideas?

I think you may need to initialise the motor. I can't find the details at the moment but will send them when found if your problem is not fixed yet. Actually, I think it is in the Haynes manual....if you have one

maybe the power cuts off to early for them

I just read somewhere that if you put the window all the way down, press and HOLD the window up button down completely(as in "auto up" for 15 seconds AFTER the window is completely up, you will reset the travel on the window.

I did this last night for all my windows and the one touch close works fine. I didn't try it with the power lock function, or the "ALL WINDOWS" button, but the one touch for individual windows works for all now. I'll try the auto locking tomorrow...