You should note what model Eagle you have. If it is an HT, it doesn't have the control panel (or valves) others are showing. But the water in and the black tank flush are on separate sides of the fifth, so hard to confuse.
If the pump runs, but you are sure all the water is off, then you have a leak. Since it is the black tank that is filling, it is has to be the toilet (which is the only thing that drains into the black tank, everything else goes to the gray tank(s)).
But - how long does this transfer take? A few hours, overnight, or a couple of days? If days, you may just be using up all of your water, and filling the black through normal use....
2012 Ford F-150 Eco, Max/Max
Jayco 26.5 RLS, Reese Sidewinder