Bob, I think you need to read some things again...
You said, "Where does the water from the discharge hose GO, once it gets past the Joker valve? If you said: 'Into the tank', you'd be wrong. It goes to the 'flapper valve' or, more properly (because I looked it up!) the 'Base Valve Gasket', which is part # 16 in the parts diagram in the link below."The joker valve is in the fitting that attaches the head discharge hose to the pump...once the waste gets through the joker valve, it's in the head discharge hose...no way can it go back through any part of the pump once it gets into the head discharge hose. Nor does the pump put any suction on a joker valve Pumping the toilet does not cause it to 'sucks' itself together, forming a seal"...it's just a rubber cup with a slit in it and "lips" on the outside that make it a one way valve--at least until the slit becomes so stretched by waste passing through it that it's become a gaping hole instead of a slit--that has only one function: to BLOCK a major backflow due to backpressure downstream of the toilet from flooding the bowl. It isn't supposed to prevent slow seepage, although a brand new one might for a short time. Whether the pump handle is left in the up or down position between uses makes no difference whatever. And flapper valves don't rotate...they're actually just a square flat "gasket" that has a weighted "tongue" (the flapper) dangling in the middle that causes it to function as a kind of one way valve, though not a very efficient one. Water backflow from the head discharge hose has no trouble getting past one into the bowl. You are correct, though, that removing the joker valve will have no impact whatever on whether the pump pushes waste out OR pulls flush water in. In fact, many owners of houseboats and other larger vessels that don't heel who want their toilets to hold water "like the one at home" remove the joker valve and install a loop in the head discharge line that's about as high as the bowl...allowing the water in the line between the toilet discharge and the top of the loop to run back into the bowl.Most manual marine toilets--good quality AND junk--have piston/cylinder pumps that all work pretty much the same way...the only major difference is how efficiently they do it and how durable they are: A piston rod inside a cylinder pulls water in on one stroke and pushes it out on the other stroke. Manual toilets are “double-action”, that is both sides of the piston are used simultaneously for different purposes. When you pull the pump piston up, a vacuum is created in the space below the piston which pulls some of the contents from the toilet bowl and into the bottom half of the pump cylinder. Then, when you push it down, a pair of built-in valves (the flapper valves you referred to) reverses and the material is pushed out of the bottom half of the pump, through the joker valve and on to a holding tank, treatment system, overboard or other ultimate destination. When you pull up on the pump in the "wet" mode, any water in the top of the cylinder is expelled through a flapper valve and connecting hose, to the entry point at the rear of the toilet bowl to rinse the bowl. Pushing the handle down creates a vacuum in the top half of the cylinder and pulls in outside water, filling the empty space above the piston. So you're bringing in outside water for flushing and delivering it to the bowl for rinsing at the same time the contents of the bowl are being pulled out and sent on their way. The "dry/flush" lever or knob near the top of the toilet pump operates a valve that opens (flush) or blocks (dry) the flow of flush water from the top of the pump. In the “wet” mode, the pump pulls water in from outside to rinse the bowl, while simultaneously pushing the contents out of the bowl and pumping them downstream. In the “dry” mode, it only pushes bowl contents out. While in the “dry” mode, air pressure created by pumping a manual toilet that is in good condition can move waste and water through the system up to about 6 feet without bringing in any flush water.So, Mike...if you want your head discharge line to be empty, you might try pumping longer in the dry mode. If the uphill run to the tank is much more than about 6', consider putting a loop in the line that's closer to the toilet and slightly above the tank...flush long enough to get bowl contents over the top of the loop and let gravity get it the rest of the way to the tank. On sailboats there really should have a loop in the line anyway...to prevent waste in the tank that gets into the line when you're heeled from getting back to the toilet.Meanwhile, when the boat will sit, follow the clean water with a cupful of white vinegar flushed all the way through to the tank to prevent sea water mineral buildup in the pump, joker valve and head discharge hose. As for the original poster's problem... His bowl is filling up almost immediately after flushing...so if it really is backflow of bowl contents, the first thing I'd check is the tank vent line.