When you had the panel off did you drive around like that for a while, operating the window?
My PO had an issue with the drivers side (before my time) where the evidence of a brazed repair was clear after I took off the panel - one of the regulator mounting bolts worked the mounting hole larger and everything would move about when the window peaked and then the next time would not go up high enough to close.
I've ahem had a piece of hardwood stuffed in the door to make the regulator stay in the right location for several years.

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95 E300D gave away
77 300D, 227k, station car
83 300CD 370k, body gone away to the rust gods, engine is in a Yota pickup, going strong
89 190E 2.6- 335k, no more
79 VW FI Bus- 154k summer driver
59 VW Beetle ragtop- 175k
12 VW Jetta- 250k
74 MG Midget-78k