On my 01S, after I unlatch the convertible top, the windows will drop down and stay down until the convertible top is fully open. While the top is partially open, I cannot raise the windows using the window switch.
There is a position sensor in one of the B pillars that tells the car whether the top is fully open. See this post
http://986forum.com/forums/general-discussions/24173-b-pillar-micro-switch-98661310102-a.html
Perhaps this sensor isn't working or the alignment has changed somehow.
My guess is the sensor does two things. It tells the motor to stop and it tells the light on the dash to go off. If both these things are happening, then I'm not sure where the problem might be.
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