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Sounds like a gas leak to me, if you're only touching the fuel system between not starting and starting. Check the carb throat for fuel after cranking in addition to the spark plugs.
Do you have a shutoff valve between the fuel tank and the filter?
If I understand correctly, the fuel system should be full of fuel and free of air at all times. I don't recall ever pulling off a fuel filter and finding it empty, or even near empty. If your fuel filter is empty after sitting for some time the fuel must be going somewhere. Is the filter the highest point in the system?
Is the carb bowl full of fuel when you return to the boat? If it is, there is likely enough fuel to get the engine running, and I would think you would experience a shutdown shortly after starting as that big air bubble works its way through.
Others will be along with ideas I'm sure. If you return to the boat to an empty fuel line the fuel must have gone somewhere. My guess would be into the bilge, or back into the tank if there is no shutoff valve (or the valve is left open).
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