I've never had a Boxster window mechanisim apart...and assuming you assembled it correctly, it sounds as if the window motor has been polarized to turn in the opposite direction. Prior to alternators, when cars had generators you sometimes had to polarize the motor/generator to function properly. If memory serves, you had to connect the ground lead to the motor to a negative battery lead and briefly touch the positive motor lead to the positive battery post. Just a thought.
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