I flush the head via fresh water before leaving the boat. A lot of it really depends on where you're sailing, since different waters have different critters in them. Have you tried closing the through-hull while still out on the open ocean, to see if the cleaner water out there helps keep the line from stinking as much...might be worth a shot.
BTW, you can generally prime a head by dumping water directly in to the bowl IIRC, but YMMV depending on which head you have.
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You know what the first rule of sailing is? ...Love. You can learn all the math in the 'verse, but you take
a boat to the sea you don't love, she'll shake you off just as sure as the turning of the worlds. Love keeps
her going when she oughta fall down, tells you she's hurting 'fore she keens. Makes her a home.
—Cpt. Mal Reynolds, Serenity (edited)
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Still—DON'T READ THAT POST AGAIN.