I had this same issue in my 98 Beetle -- While my car was in the shop for some heat/ac problems (not related to all of this but: check your radiator fans! the Beetles apparently have a common problem with the separate fuse box for the fans pulling too much power to the fusebox and blowing a fuse and starting to melt the box, so check it! if you find yourself having an overheating problem this could be it) ANYWAY when my car was in the shop getting my heat/ac fixed, I asked them to fix the windows for me and when I got it back they said they just had to replace the tracks and make sure it was lubed up
There are a couple of possibilities.
Either the window is out of adjustment and has track problems, or the regulator is worn out.
Either way you need to take the inner door panel off, by removing the screws on the handles, etc., and then unsnap the clips around the front, bottom, and back. Then lift off because the top sort of hooks on.
You will see that the metal on the bottom of the window is attached to the regulator mechanism. Detach that, and then you can push the window up and down by hand, from underneath.
This will tell you if the window is binding or track bad.
Some silicone lube on the tracks may help.
Then you can look at the regulator to see if the twisted wire linear gear is stripped or not, and if it has to be replaced.
Is it gear operated with a crank or 12volt operation...in any event, I would take the door panel off after removing the handles, door opener, and window....then check the linkage for bends, breaks also check the continuity of the window related to the channel it runs in....rusted, dirty, clogged up>?? they must be perfectly aligned to work properly...Thanks, wz
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