Sven says when lowering the top the compartment cover closes but the bow/rear window does not lower. This implies the controller does not recognize the cover as being locked.

The controller receives inputs from each lock left and right. These are A24s2 and A25s2 in the documentation. One or both of these switches is probably not closing. This would be confirmed by codes of 2 and/or 3 from pin 10 of the diagnostic connector. Also, with the top completely lowered by hand the red lamp in the top button will be on if either A24s2 or A25s2 is open.

Sven, besides getting the codes I would verify that the compartment cover is mechanically locked. Take your tool for working the locks and manually lock the cover down on either side. You will hear a pronounced "click" as each one locks. Then try lowering the bow automatically. If it works, your problem is not the lock switches.