My S Reg 323i electric roof.

Ive had the same problem on my car. If you open the trunk and pull away the material covering on the left hand side you will find two electric motors similar to the ones that winds the windows these motors have to be in exact sync for the whole system to work fine.

The one drives the lid and the other one drives the roof. You can engage and disengage the motors to get the roof in sync and working perfectly. Also check that when the lid closes it engages a button on the left that allowes the roof to close aver the lid after the lid has closed this button also tells the car that the roof lid is closed and it is ok to let the trunk be opened.

I also suggest that you treat the roof mechanism with some penetrating oil.