You can put an Allen key into the motor and manually close it? Was the car on the road? I know when I first learned to drive I used to drive me e34 through huge puddles just for the splash and would regularly lose windows and sunroof. I've since grown up, marginally. Check that the splash guards are all in place properly. I for some reason think that water was getting in on the passenger side (possibly to the relay box on the passing side). I never checked out was there a leak but in a few days it used to sort itself out.