Thanks guys. I'll update you when (if) I solve the problem. This site has been enormously helpful to me in bringing my head into the 21st century.
Answering some suggestions: I have a vented loop on the overboard discharge, which diverts off the tank line with a y-valve (handle removed). The tank inflow does not have a loop as it does not go overboard and cannot siphon seawater into the boat. This backflow occurred while testing the overboard discharge with seawater only. It happened slowly, I didn't notice the extra water in the bowl until later. After that I pumped some air through the line by operating the pump. That seemed to solve it. I don't know if the valve cleared or the water was just all overboard.