The flushing may not be so necessary at this point Lorne..for a few reasons.
I would try a couple things.
First, I would run clean water with
bleach in a sink or tub for 2 or 3 minutes to clean/freshen the ejector pit. (if you can freshen an ejector pit...

).
Then I would remove the glass cover and physically engage the pump to pump out as much water/effluent as possible (use anything to reach down and engage the pill switch or the float switch).
Then I would unplug the ejector pump (will need to monitor water level periodically because of this).
Then I would mark that lowest level with a permanent marker (use flashlight to see well).
Then I would install the glass cover again (to your health..

)...
and would not let anyone near that bathroom for a couple days (I might even shut off all shutoffs to toilet and sink...and tape off the tub/shower valve).
Then 24-48 hours later...if you come back..shine light through the GLASS COVER (I love that by the way...makes this easier!!) and you see that the level is different than marked...well...
ONLY TWO THINGS THAT COULD CAUSE THAT:
(1) Defective check valve with blocked drain line backing up and draining past the defective check valve.....OR...
(2)
There is ground water seeping into the tank as you suspected.
I'm going with #2 for now.
I say we take this step at a time....next step will be determined by what happens...? Maybe nothing...? Hmmm...??
Let me know what you think...Mark