Just had the same problem with my 2000. It was one of the pulleys of the window regulator, it needed oiling. You have to take the door panel off to get access to the regulator and then oil the center bearing on the plastic pulleys at the bootom of the door. I also greased the rails and cables at the same time. Works perfectly now.
The best fix is to replace the regulator, but its a bit more involved than just taking off the door panel and lubing.
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Current car
2000 Boxster 2.7l red/black
Previous cars
1973 Opel Manta
1969(?) Fiat 850 Convertible
1979 Lancia Beta Coupe
1981 Alfa Romeo GTV 6
1985 Alfa Romeo Graduate
1985 Porsche 944
1989 Porsche 944
1981 Triumph TR7
1989 (?) Alfa Romeo Milano
1993 Saab 9000
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