Any chance that the shaft seal is dripping faster than it should?
At rest it should drip 2 or 3 drops per minute. If it is dripping faster it should be tightened (or packing replaced). It is amazing how fast the water accumulates in the bilge. Leave the bilge pump in the auto position.
In my opinion it is common to have water seep back into the mufflers when sitting in the water. the main point of the flappers is to prevent a wave to force water back up into the engine.
STARS AND STRIPES FOREVER