My S had this problem when I first bought the car then after a few days it went away. Now the problem has come back.

When you hit the auto roll down on the driver side window, or open/close the top, the driver side window rolls part way down and stops. I hit the power window button again and it goes down part way.

Anyone ever have this problem?

 

This is a commonly reported issue with earlier cars. No surprises here. Your window regulator is on its way out. The auto-down feature is acting up and will eventually stop working all together. You can try a temporary fix but there's no telling how long it will last.
https://www.s2ki.com/forums/index.php?showtopic=131795
Eventually, you will need a new regulator or you can equip your car with an "Autoloc" device for about 50 bucks that will give you back your auto-down and also add auto-UP.

 

there is a TSB. check the library.