If the brakes are squealing, there's a good chance it is the brake pad wear sensor. A new design was implemented in January 2006 and can be identified by its green color.
Car problem reports
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Most reported BMW 545i problems
A creak or squeak can be heard from the top of the front or rear doors. This noise is most noticeable when the windows are fully up. The noise is caused by the decay of the flocking material on the door seals. New door seals, Teflon tape, special lube, or a combination of all of these may be needed to eliminate the noise.