Im willing to bet it has nothing to do with the head unit. If you have the 2 piece setup (Im pretty sure you do), it is most likely the tuner/amp in the storage compartment in the rear (I think they are back there). But before I would check that, check the fader switch in the center console. They are known to cause issues like this. Id pull out the fader switch and clean it with contact cleaner and give that a try.

good luck

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93 300D 2.5 Turbo, Black/Palomino 273K
09 E350 Black/Black 41K