Right above the right side of the a/c control unit, there is a vent. A whirring noise is coming from this vent. I assume this is some sort of air sampling fan or something.
A small fan that cycles air through the A/C thermostat may be the cause; replacement is the answer. It's not horribly expensive, just a lot more than you think it should be (what else is new?)
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2005 S500 4-Matic
with Gateway 500 iPod integration
Formerly: 2000 S500
with Ice>Link iPod integration
Moto V710 phone with MikBox
Upgraded Voice Control
it seems to be a part of the a/c unit though. I don't see a way to replace just that. Seems like the whole climate control unit needs to be replaced at about $600.