my 92 400e does similar.... a muffled "thud - thud -thud" when the heater temps are used. I've also noticed that I do not have airflow from my passenger floor vent...

Could that be the vacuum attempting to open a stuck passenger floor vent flap? If so, is it accessable for easy repair?

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Jeff
'87 300E
'92 400E
'06 ML350