The flappers prevent water from purging into your exhaust manifold and filling a cylinder. This is possible but not limited to sudden shutdown of engine underway, plugged exhaust system or just plain old coming off plane too quickly while setting up shop...
Your v6 could be having back pressure problems. When you're boat is in the water you have resistance against your exiting exhaust. On muffs you will have little to no resistance.
Maybe someone else with v6 knowledge can step up.
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