It can be as simple as the switch that tells the roof mechanism the E brake is on has broke. I would just take it to any Porsche or Euro car repair and have them give you a quote to fix it, then do it yourself if possible. According to my books, the top can be very difficult to work on. Good luck!
'04 Boxster S 50 Jarhe 550 Spyder Special Edition 851 of 1953 made, 3.2L, 6-speed manual short-throw
'Cause you know the Germans make good stuff!!