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I had a new regulator installed in my 99 beetle about a month ago.. The body shop that put it in never could get it to work, he said you had to undo the negative side of the battery to make the window rollup and down..then it would quit and you had to do that again.. Well I tried that and never could get the window to go up or down.. This morning I stuck the key in the door to unlock it and both windows rolled down.. I turned the key back in the position to lock the door and the drivers window rolled back up..?? Any ideas what is going on here ? Thanks!
 

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Have you scanned the car with a vw compatible scan tool? If so; what are the trouble codes? Wiring harness problems are common and a incorrectly installed part or poor quality parts might be a issue. The primary issues with door accessories not working; typically narrow down to: harness broken/compromised, door lock modules failing, comfort control module problems and window regulator failures.

A vw compatible scan tool; can help, narrow down the problem if it is throwing a trouble code. Specific electrical component failures; will typically throw a trouble code (e.g. door lock module, window regulator, comfort control module, etc.).

I also; wonder what brand regulator they put in and if it is the right part for the car?
 

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Sounds like you may have few problems. If you did not hold the key in the lock in the unlock position, then I would say the door lock actuator is bad.

BMW is famous for similar problems where the Hall Effect switch on the door lock actuator goes bad and the windows and sunroof will open on their own without anyone around.

Which window regulator was replaced? Drivers or passenger?

There could be a problem with the Convenience Center module with it part of the drivers window motor as I recall?

Agree that something like the VAG401 or VCDS may offer more insight if there are specific codes. I also do now know VCDS very well but it may offer bi-directional support where the software can command the window(s) up and down to help narrow down control module or actual wiring problems.
 
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