This will sound bizarre... have you checked the handbrake adjustment? i say this because i had a similar sounding noise on start up(minor clunking noise) or turn off and traveling over larger bumps as you describe,after some routine brake maintenance at the dealers the noise vanished.
Try applying the handbrake a couple of notches then open and close a door a few times to see if it makes the same noise.
old E30 beemers were the same,creaks when the handbrake is on as the suspension moves(usually when getting in the car)