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Ugh, I've been involved in problems that deify logic before. Did you send your old unit to Beckman for testing?
The vent flaps have position sensors ( potentiometers ) in addition to pots on the dash face to control air , I'd probe the voltages / look on the HHT at the values. I'm wondering if when run in manual HHT mode they are ignored but when run through the climate control buttons it cause a problem.
I'd also change the version coding to something else and check the results ( I don't think anything will "burn up" if this is done. Remember, this unit was also used on similar year C class. ( E class is different )
I've got 2 wiring diagrams of that area R23/1 though 3 are the vent flaps , r 1 through 3 are the dash knobs,
83 Climate control
83.40-U-2000YB Air conditioning (automatic) AC MY 1996
83.40-U-2000YC Air conditioning (automatic) AC As of MY 1997
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