Have you tried to reset the window switches?
go to:
http://www.300cforums.com/showthread.php?t=1004
and scroll down about 6 posts to the post titled "Standard Procedure" to be followed after each battery disconnect.
It tells you how to reset the power windows. That will probably fix the problem. Also, please be careful to avoid hitting the power window lock switch, it isn't marked too well and sort of sticks up to be bumped on. (Happens to me, too).
Also, do remember that the power switches, now of a new safety design, require a pretty good pull or push to function. The front ones, in the detent position, force an automatic full up or down without further touching the switch.
While you are resetting, if your steering wheel isn's exactly centered, try doing that reset proceduce which is also listed in the same post.
IMO, that post should be printed out by everyone and kept in the glovebox. I have had to use it anytime a techie works on the car; they almost always have to disconnect the battery and most of them don't know how to reset these features. They are messed up just about everytime the battery is disconnected.