First, let me say....this is definately the most confusing post in the forum!!!!!!!
My 93 300SE has the same problem on the front passenger window. It Goes up, then comes down about an inch or two....ONLY IN AUTO MODE. The problem does not get worse or better with time. A technician at the dealership is a good friend of mines, and he said not to worry about it unless i use the remote express opening and closing consistantly (this is where you can put the windows and sunroof up and down with the remote and key). He also said, it is a problem that is not really worth dissasembling the door for. If you can, just live with it, if not, the door must be dissassembled.
Also, to fix your Pneumatic assist in your door, MAKE SURE KEY IS NOT IN IGNITION!! Go in the trunk and pull fuse #9. Wait ten seconds and replace it. This should fix it!