I have been through this when my 2000 E320 was only one and a half year old. Warm air was blowing on the driver side and cold air on the passenger car. The technician didn't seem to know the basic cause of a low refrigerant charge and dismantled many parts to check for sensors. At the end, having less than 1 pound of refrigerant was the cause (normaly 2.2 pounds if I remember well).
It took many more visits at the dealer to discover a faulty expansion valve (rare on this car then) and replace the long high pressure hose and the dryer. The problem took 3 years to solve while the car was always losing it refrigerant very slowly. It has been quite a bad experience.
Xenon/washers, Rain-sensing, Sunroof, Rear sunshade, Rear reading lamps, Bose, Cd changer