Several possible causes...
But if you're on Lanier, we can eliminate most of 'em 'cuz you shouldn't have any macerators, y-valves or discharge thru-hulls. So my first inclination is toward intake water, not a back-up from your holding tank. If your bowl is below the waterline and you don't have a vented loop in the intake between the pump and the bowl...and if you leave the intake seacock open when the head isn't being used, water can very easily rise in the bowl to the waterline on the boat. If that's above the top of the bowl, leaving the seaock open is a good way to sink your boat. It's POSSIBLE that a full holding tank expanded a bit in the heat and backed up into the head discharge line. However, it shouldn't have made it into the bowl unless your head joker valve needs replacing. A more likely scenario: There should be a vented loop in the head discharge line that's at least a foot above the waterline at any angle of heel. If you're like 90% of boat owners, you quit pumping the toilet as soon as the bowl is empty, leaving whatever was in the bowl sitting in the line right next to the head instead of flushing it all the way through the system and rinsing the hose. The next person does the same thing...and the next...keeping the line between the toilet and the top of the loop full of sewage. (That also contributes to urine crystal build-up in the hose, but that's another issue). If the joker valve leaks, it's all gonna run back into the bowl...and a little bit of paper or solids stuck in the joker valve can easily keep it from closing completely. When you pumped it all out of the bowl, you dislodged or washed away whatever it was...the joker valve stays closed now...and you're left wondering why your bowl filled up. That's my guess from here, without seeing your installation.
