I also experienced the same problem where the top went down but the trunk lid would not come down. I went back and checked and I had my coat lying on top of the cargo cover. It was a thin coat but thick enough that the top wouldn't go down far enough for the trunk to close. Moved the coat and problem solved!
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Garage:
'11 Z4is
'09 Audi Q5
'07 Lamborghini Gallardo
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