Most likely cause is dead sea creatures {tiny plankton etc) in the flush water. Mine does this every time I flush after the boat has been sitting unused. If I'm out cruising and using the heads regularly the smell stops until the boat sits unused again.
Odor from sea water left to sit and stagnate goes away after the first use when you come back aboard flushes it all out of the system. He said he experiences it every time the toilet is flushed.
I'm contemplating setting up a freshwater flush line for each head to use when I know the boat will sit unused for a few days.
I hope you're not considering connecting your toilet to the fresh water plumbing, Kevin. However there is a safe way to supply fresh water to a sea water toilet without doing that: Tee a y-valve into your head sink drain line and also one in your toilet intake line as close to the intake thru-hull as possible and still be accessible. To rinse the sea water out toilet and all its plumbing, close the toilet intake thru-hull, turn the y-valves to direct the flow from the sink to the toilet intake line, fill the sink with clean fresh water...flushing the toilet will pull the water out of the sink, rinsing out the whole system--intake line, pump, channel in the rim of the bowl and the toilet discharge line. Just pouring water into the bowl and flushing only rinses out the toilet discharge line.
It's easier re-plumb if your head sink drain thru-hull is below-waterline (which it is on most sailboats, but not common on powerboats): just re-route the toilet intake line to tee into the head sink drain line as close to the thru-hull as possible (this frees up a thru-hull for other uses, btw)...it needs to be below waterline. Flush normally with sea water till you're ready to close up the boat. Then close the the thru-hull, fill the sink with clean water...flush the toilet. Because the seacock is closed the toilet will pull the water out of the sink, rinsing out the whole system.