I used to own another E60 that also rattled a lot, looked like it was coming from the drivers side A/C vent or somewhere there . . . never discovered what was the issue, the rattle used to be really noisy when driving in rough roads (I'm talking about not "smooth" roads). It was really annoying, specially when not playing music.
I always thought it was the A/C vent having loose parts inside. Who knows.