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Sometimes the foam that is used to seal the flaps, will fall to bits over time ,and can jamb the flaps, a airblower blasted up the feet vent holes while working the flaps can dislodge it, but if you have it working good now, leave it alone , as you could also blow the foam off ,thus creating a problem.
What you have said makes perfect sense. It was after a full on bumpy ride that it started happening (the truck is 25 years old next month). I ended up actually disconnecting those levers because I broke the little plastic knob that guides its way through to open and close. I can see that it is out of alignment, probably because the foam is dislodged. I am not concerned though. At least I can get the air back up on the windscreen for demisting now