To Tintin:
You need to replace the boot locking mechanism (something called ZZH, or "Zuziehhilfe". Don't you love German words?). It's no big deal, though I don't have a clue how much VW will charge for it. I've had this issue with an early production car, and the solution was just swapping parts. The locking mechanism has a sensor that tells the car when the boot is closed. Without it there's no roof operation possible.
To ububba:
You have a mechanical problem in the roof system. One of the hooks that hold the trunk lid while the roof is operating is apparently not releasing. As far as I can recall, the hook is spring loaded to close, and power operated to open, so if it's not opening completely, there's something wrong with it. It has happened that, as the hook's shaft is only pressed into place, it sometimes loses its position. Try opening the boot lid and compare the rear-most side hooks. They may show signs of wear, or may be in different positions. If that's the case, you may have to replace the one that opens the least