My new filter "Premium Guard PureFlow" (PC99238x) has the arrows pointing up. Thankfully the instruction page has the phrase: Insert cabin filter with the arrows pointing to the floor.
Did you ever had to replace the HVAC circulating actuator on yours? It’s located left to the cabin air filter. Mine makes this flapping noise once the car is off.
I never had to replace the actuator. It would make noise when the temperature outside and the inside set point were close. It would seems to lose its mind and click consciously a few degree change of the inside set point would claim it down.