I'm only guessing, but if I understand you correctly, I'd say your back flaps are slamming shut (as they will) choking off the engine like a choke being pulled on a warm engine still pulling fuel. But man, I'm really reaching without being there. . . .
Maybe I'm going the wrong way with those air doors.. when I had the air filters off the other day they were barely bobbling when I opened it up. I never seen them really like flap wide open...