Mine doesn't leak at all (knock on sycamore)
And I never hand-wash my car -- I always take it to a hand-wash place near my office. Come to think of it, my E46 convertible never leaked for the entire four years I owned it either -- and that was a soft top. You should take it to the dealer and have them adjust the rubber weatherstripping for you.
Quick question -- do you think it's possible your painter incorrectly re-installed the rubber bits after painting your trim black? Or maybe damaged them in some way?