I have a 2006 Cab and the top has been up for the past year. Now when I put it down there is no problems but when I put it up the latch goes up and down on the window shield. I can stop it with the bottom but the windows do not go up automatically. What could be the problems?

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Could be a faulty microswitch in the roof frame or that the latch is not pushing in far enough. If you push up on the latch catch while holding the button do the windows roll up?? If so the microswitch assembly is likely faulty. Could also be the latch but the microswitch is more likely the culprit.

- Casey

Make sure the plastic cover is on the latch hook. If it has broken or been lost the hook will not reach the switch to complete the cycle.
http://bethnrayndogs.com/car_docs/Porsche/porsche/Porsche_Tech/Porsche_TECHNICAL_BOOKS/Tech_Bulletins/Grp6_13-98.pdf

Also here but damn hard to find.
http://www.pelicanparts.com/cgi-bin/smart/more_info.cgi?pn=996-561-787-01-01C-M100&catalog_description=&Convertible%2520Top%2520 Latch%2520Arm%2520Cover%2520