You might watch this video and follow the reset procedure, see if that helps.
If the adjustments don't help; you might scan for any trouble codes with a vw scan tool like vcds by ross tech. If you have a failing window regulator, motor or other related parts; it may not allow the adjustment to be done correctly and this won't come down, to clean the convertible like it should. Let us know if the adjustment procedure works and we can ho from there. Thanks.
I have a 2003 gls convertible and the passenger window quit working and the top would also not go up or down, after reading a tin things online I took the door panel off and unplugged the window motor and replugged it in. Magic! Both the top and the window now work. Hope this helps someone.
That probably reset the com network for the comfort control module; is it still working correctly? Many times, a hardware or wiring failure; will bring down the network, things will atop working (aka: "single wire mode").