Cloged vents do cause this to happen but I don't think it could be the vent because if it was you would have the same problem while fueling on the trailer as in the water, you mentioned that you only have the problem while fueling is in the water. My money is the angle of the hose is effectively flat it has to go uphill slightly while the boat is in the water due to the static trim condion of the boat while in water. See if you can re-arrange the hose slightly. (this can be difficult, I know)
One way to test this is put a lot of weight in the stern the next time you re-fuel. (Bring along a lot of people and fill bait tanks with water ) If the problem goes away...then you have your next winter project...re-install fuel line
(This happened on a boat I had, I ended up installing a new (slightly shorter) line ans was able to pitch it more and the problem went away, could then re-fuel as fast as the pump could pump.)
By looking at your avitar, if that is your boat, you have a lot of weight forward...
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