Smell starts in the head but very quickly consumes entire boat though the boat isn't all that big, the maximum distance from that head to anywhere else on the boat is no more than 12 or 14 feet.
Holding tank is in direct center of boat.
I have seen black flecks from that particular bowel.
Hoses are 7 or 8 years old.
Boat has always had a boat smell but not a sewage smell.
after pumping out I noticed a tiny leak from the overboard discharge macerator - maybe from the suction of the dockside pumpout hose? Never noticed it before. That Jabsco macerator pump was replaced around 5 years ago.
I'm pretty sure you have more than one problem:
The black flecks in the bowl are the remains of dead, decaying and STINKING animal or vegetable sea life trapped in the intake line and/or the channel in the rim of the bowl.
The cure: remove the head intake line from the thru-hull (close the seacock first!) and stick it into a bucket of water to which you've added a quart of distilled white vinegar. Flush the entire bucketful through to the tank.
Install a strainer in the intake line to prevent this problem in the future. It needs to be above waterline and accessible for cleaning it out on a regular basis.
I strongly suspect that your hoses have permeated with odor. If so, there will always be at least a little odor in every locker or area they pass through that you may not notice except when that locker is open or when the toilet is flushed. You have horrendous odor when you flush because waste or water being pushed through a hose puts pressure on the hose walls, pushing out odor. They're most likely flex PVC, which have almost -0- odor permeation resistance, but even if they aren't, 7-8 yr old hoses are close the end of the working life for any hose (10 years), so I strongly recommend that you replace 'em. Raritan SaniFlex
RaritanSaniFlex hose is the best, has a 10 yr warranty against odor permeation and has the added advantage of being so flexible it can be bent almost as tight as a hairpin without kinking, making most rehosing jobs a LOT easier. Defender has it for <$10/ft and sells it by the foot.
Raritan Sani / Flex Sanitation Hose at Defender
How far--how many hose feet--is that toilet from the holding tank? I'm asking because 6' is about as far as the average manual or electric toilet can move bowl contents without a lot of help from gravity in the amount of time anyone wants to leave their finger on the flush button unless you want to fill up the tank with flush water. Each flush should be followed with enough clean water to rinse out the hose anyway, 'cuz waste left to sit in the hose will permeate all but the most odor permeation hose.
That leaking 5 yr old macerator pump is definitely a source of your odor! Jabsco macerator pumps have an average trouble-free lifespan of only about two years especially if they aren't used because the rubber seals and gaskets in 'em dry out and fail. Jabsco has a rebuild kit for it, but I'd replace it with an electric diaphragm pump that can run dry without harm and can easily last at least a couple of decades. The Dometic T-Series Pump is the best one.
SeaLand T-Series Pump at Defender
I usually put a little water down the hose after pump out to clean out the hose.
You should be putting enough water into the tank via the deck pumpout fitting to cover the bottom of it to a depth of about 4" and pump that out or turn on the macerator pump to flush any sludge out of the bottom of the tank.
We can address your "boat smell" after we solve this odor problem...although you'll find solutions to that in my book (see link in my signature...just click on the title). I"m always glad to answer questions whether you have my book or not.
--Peggie