i had a similar issue on my 335i. The dealer fixed it by tightening the struts that connect the firewall the the strut towers. Apparently one of the techs didnt torque them down enough after replacing a fuel and oil sensor.
Again i dont know why it would cause the noise but it definitely sounded like one of my accessories was about to die/fall off.
2008 e90 M3 6MT EDC/Premium/Cold/Nav Jerez/Black/Alum
2007 e90 335i 6MT Sport/Premium/Nav Blk/Blk/Alum SOLD