"In theory, when you are pumping (sucking) shouldnt the little rubber flapper valve be sucked closed? releasing when you quit sucking?"
Only if the vented loop/anti-siphon valve has been installed in the intake line between the thru-hull and the bowl, which is the wrong place for it. It belongs between the pump and the bowl, which requires replacing the short piece of hose the toilet mfr uses to connect 'em. The installation
instructions for every manual toilet and all the basic electric toilets include drawings that illustrate the correct location for the vented loop in the intake.
An anti-siphon valve only breaks a siphon in a line through which water is being PULLED...it doesn't interfere with water being PUSHED through a line. The pump PULLS water from the thru-hull to the pump, then pushes it from the pump to the bowl. The air valve in the vented loop in a line through which water is being pushed won't open....vented loops only squirt if there's no air valve.
However, some electric toilets only have one intake line--the one from the thru-hull to the pump...it's the only place a vented loop can be installed. That requires an electric solenoid valve that's wired to the flush button..the solenoid valve closes the air valve when the flush button is pushed...the air valve opens again when the flush button is released.