The Jabsco 29090 isn't a "classic" toilet, it's the current "Twist 'n' Lock " version
Jabsco Twist 'n' Lock Manual Toilets Your problem isn't in the toilet...it's in the flush water plumbing TO the toilet. If you look at Figure 1 on page 3 of the manual at the link I included, you'll that there's a vented loop in the flush water intake line (ignore the one in the discharge line...it's not needed in toilets that flush only into a holding tank). It's missing on your boat...installing it is the cure for your problem.
It needs to be at least 6-8" above waterline AT MAX HEEL, not just when the boat's at rest..which puts it about 2-3' above the bowl on most sailboats. That requires replacing the short piece of hose tha ttoilet mfrs used to connect the pump to the bowl with two lengths of 3/4" sanitation hose long enough to put the loop where it has to go.
I'm also wondering if you know what the little lever on the side of pump at the top does..
That's the wet/dry control (aka "dry/flush" control on some toilets). It only allows flush water to come in when it's in the "wet" or "flush" position...blocks the flow of flush water when in the "dry" position. It can fail with age, but that's only one of the reasons that it's NOT a substitute for the vented loop because people can accidentally leave it in the wet mode, but it does prevent water from filling up the bowl while it's in the dry mode. If the the wet/dry lever doesn't block the flow of flush water when in the "dry" mode, the lever isn't moving the cam to block it.
A vented loop's primary function is to break a siphon... Priming a toilet pump can start a siphon. The loop offers the added protection of creating a "hill" in a line that's too high for rising water to climb over. It also provides a fail-safe that a properly working wet/dry valve can't: it keeps water out of the bowl if the wet/dry valve is left open...which can happen 'cuz humans are fallible. If they're lucky, people are aboard to notice that shoes are afloat in the cabin.
And that's my lecture for tonight...question are welcome.
--Peggie