The flapper does get above the surface of the water. But the water level
never drops low enough for the flapper to close. The water level only goes
down to a height of maybe a couple of inches.

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The only thing that brings the flapper back down into the sealed
position is the water level dropping low enough to expose the flapper
above the surface of the water. Is the water escaping fast enough
to expose the flapper? The inlet water should not overcome the
emptying of the tank.