When I first start out driving my transmission makes a whistling noise. After a while the noise stops. The car doesn't seem to have any problems with the driveability, performance, etc.
Are you sure that the noise is coming from the transmission? What makes you think so?
A very common E60 problem is an intake manifold vacuum leak. It will whistle, but only when cold until the parts expand and reseal the intake. Usually this is accompanied by check engine codes indicating "lambda sensor out of range", only at idle and only when cold.
It's a sizeable job to remove the intake manifold and replace all the rubber gaskets and most people replace the PCV Plate at the same time.
No. I think what he was alluding to is the whistling automatics. It seems to happen after the filter is replaced with an aftermarket one. But the problem isn't actually the filter. It's the aftermarket o-ring that comes with the filter. After folks replace the o-ring with an OE BMW one, even the aftermarket filters are quiet.
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