The possible explanations
The most likely on--and if the water was clean, the only possible one: human fallibility. Although you're usually careful to close the intake seacock, you forgot to do it when you closed up the boat last time--or you didn't close it completely. Without a vented loop in the head intake that's higher than the boat's waterline, water outside the boat did what water does--it sought its own level inside the boat. That's the #1 cause of boats sinking in their slips. You're lucky that your bilge pumps kept up with it.And btw, anyone who relies on the wet/dry valve to protect your boat instead of closing the seacock when you leave the boat is playing Russian roulette...'cuz dry/flush valves--especially in Jabsco toilets--have a very high failure rate and the human "failure" rate (last one to use to the head, especially if it's a guest, forgets to leave it in the dry position) is even higher.The fail/safe solution: install a vented loop in the head intake that's at least 8-12" above the waterline at any angle of heel. It has to go between the pump and the bowl...if you put it between the thru-hull and the pump, the pump can't prime.Only if the water was dirty could it have been backflow. And a joker valve in good condition is only supposed to prevent an immediate rush of water back into the bowl in the event of a clog or backpressure...it's not supposed to prevent slow sleepage, which is most likely to happen while you're away from the boat. If the water was dirty, only a few things could cause it: 1. The distance from the toilet to the tank is very long and runs continuously uphill (and, btw you shouldn't have to ask how your own plumbing goes...you should know every inch of your boat). The cure: a vented loop in the head discharge--also at least 8-12" above the waterline at any angle of heel--that's installed immediately after the toilet...so that there's only the water in the hose between the toilet and the top of the loop to run back downhill.2. If the tank was close to full when you left the boat, a blocked tank vent--highly likely at this time of year 'cuz dirt daubers build nests in vent thru-hulls--could pressurize the tank enough to send waste back toward the toilet. Don't try to pump out till you're certain the vent is open. Unless your boat is plumbed illegally for Lake Lanier, the following won't apply to you, but does to those whose boats are equipped with macerators to dump the tank at sea: 3. You remembered to close the head intake seacock, but forgot to close the tank overboard discharge seacock. Water rose in the tank (the macerator won't prevent it, only slow it down), overflowed it and sent water back down the head discharge hose into the bowl. Most production boat builders today don't install a y-valve in the pumpout/dumpout line 'cuz they cost more than tee or wye fittings...nor do many of 'em bother to install a vented loop between the macerator and thru-hull either. So there's no protection whatever in the system to protect against human fallibility and/or ignorance of the need to keep the tank discharge seacock closed at all times except when actually dumping the tank. Those are the only possibilities, John...it's gotta be one of 'em. If it's clean water, the head intake has to be the source...if it was dirty water, it's backflow.