My guess
If it's clean sea water, it means that water is coming in via the head intake line. Replacing the joker valve in the discharge fitting won't solve that problem.
And since any y-valve would be in the discharge line, it wouldn't have anything to do with it either.
I'm guessing that the vented loop that should be in the head intake in ALL manual toilets that are below waterline (see Figure 1 on page 3 of the installation instructions here
http://www.jabsco.com/files/29090_-_29120_-_3000_datasheet.pdf ) was never installed. Without it there's nothing to prevent water OUTside the boat from seeking its own level INside the boat via the toilet bowl if the wet/dry cam fails or the lever is left in the wet position.
(Btw, although instructions at the link I just gave you are for Jabsco's newest version of their manual toilet, the only difference between it and their previous toilets is the addition of the conical "plug" at the bottom of the steel piiston rod and the "lock" at the top of it...everything else in the pump is the same as the toilet on your customer's boat.)
Or, if the toilet is plumbed to discharge directly overboard and there's no vented loop in the dscharge line either, sea water can also fill the bowl via the discharge thru-hull.
In eiither case, I'd bet real money tha your customer isn't bothering to close the seacocks when he leaves the boat. Leaving 'em open has sunk many a boat in its slip!
As for the odor, it's most likely stagnant sea water trapped in the head intake line...the first flush after the boat has been sitting can knock you off your feet. If it doesn't go away after the first flush, there could be some dead decaying animal or vegetable sea life trapped in the head intake line. To clean it out, remove the head intake line from the thru-hull (it would prob'ly be a good idea to close the seacock first) and stick it into a bucketful of clean fresh water to which you've added a quart of distilled white vinegar. Pump the whole bucketful through the head. The vinegar will also clean out the head discharge line.
The odor MIGHT be coming back into the toilet from the tank...in which case, replacing the joker valve should take care of it. Although replacing the joker valve is NOT the cure for EVERY toilet problem, it should be replaced at least every two years--annually is better--as PREVENTIVE maintenance.
I suggest you check out the link in my signature...and I'm always available for "one on one" help if you need it.