Could simply be that the motor is wearing out. The earlier MBs use motor current as a way to check if there is something/someone stuck in the window. If the window is in auto up and there is an obstruction the motor has to draw more current to try and push the obstruction. Once motor current hits a certain point the auto up is disabled and the window stops. As your motor gets older it takes more and more current to just work as normal. Eventually you get to the point that you cannot use the window in automatic up.

The short term cheap fix is to take some silicone spray and spray the felt in the window tracks. This will allow the window to slide up easier so that the motor uses less current. Eventually you will have to replace the motor if you want to have the auto up feature.

-Jim

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1995 S350D, Green with black leather interior.
Bought January 2008 w/ 233,xxx miles.
I did 22,000 miles during the first year of ownership.