I read some years back in the Raritan instructions for the PHII ...
That kinda makes it obvious that you didn't bother to read the installation instructions when you installed it a couple of months ago.If you had, you know that you don't have a pump issue, you need a vented loop in the intake.
When a toilet is at or below the waterline, without a vented loop, there's nothing to prevent sea water outside the boat from seeking its own level INside the when the dry/flush valve is open. Installing one will solve your problem. It needs to be at least 6-8" above waterline
at any angle of heel, not just when the boat is at rest...which on most sailboats puts it 2-3
feet above the bowl. It does NOT belong in the line between the thru-hull and the pump...it needs to be installed between the pump and the bowl--see Figure 2 on page 5 in the owners manual
PH II Owner’s Manual This requires replacing the short piece of hose the mfrs use to connect 'em with hoses long enough install the loop. (See photo)
This is true of all manual toilets... if there's no loop in the intake, the bowl floods and overflows if the wet/dry (Raritan calls it Dry/Flush) valve is left open.