Our '06 X3 is also getting damped on back of the passenger side. We have sunroof (or moon roof), and we did get our back door side window smashed once in Paris, so now I don't know if it's something related to the sunroof or the new window. The new windows is not BMW original, but it's made exactly on the same factory, so I doubt it's just from the windows.
In practice the floor is always a little bit damped now on winter when it's raining, and it gets fully damped when we go through the car wash. We also need to keep the carpet out or else it never gets dry.
The funny thing is that the damp comes from the floor, not from above, as the carpet's dry on the top and damped on the rubber bottom, so it's the floor carpet that turns the removable carpet wet.
Some said it could be the draining tubes coming from the sun-roof. But you don't have sun-roof, so we might both have a case of a small defect in the window.
eh
