My UK spec E320 wagon (1995) with auto climate control (I believe you are talking about the semi-manual system which does have seperate temp controls for the driver & pass) had a similar problem--check in the area of the fusebox and brake master cylinder area when the car is running. See if you hear hissing vaccuum. There are several lines and valves (yellow) which interconnect here. Good luck

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2002 Mercedes-Benz E320 4Matic
1995 Mercedes-Benz E320 Wagon
2005 Land Rover LR3 V8 SE
1999 Audi A8 4.2L quattro