I have a 2005 325i Ci. I have water in the boot seen when it rains and the car is parked on my slopping drive. The drain holes are clear, the lights have been sealed, new rubber seals have been fitted. The inner roof cover panel has also been stripped and resealed.
The boot has been stripped out and it would seem from tests that the water is getting in through the N/S flap hinge then running into the channel were the bumper impact piston is, before it oozes out.
The inside of the car is bone dry no water on the floor or behind the seats.