I have the same problem
What happens with my boat is water siphons into the bowl when the foward water tank is full and the center tank is empty, creating a bow low or lower than normal in the water situation. To correct the problem I installed a PVC shut off valve in line with the intake to the pump motor. This would work OK except the pump is not suppose to be run dry. Several times since the installation people, including me, have attempted to flush the toilet without opening the valve.A perminate fix (if you have a par 37 series or compatable toilet) is to buy the quiet flush conversion kit from Devender, about $340, and install it with an anti siphon loop and valve, making sure the loop is well above the water line. The flush water motor will need to be installed between the intake through hull and the loop.Hope this helps.Al