Interesting question.
We had the same thing happen to us with 2 identical Shurflo pumps when the last leisure battery died. Both of these pumps draw the identical amps under load when working on the glass.
It can't be anything to do with wiring as both pumps are positioned together and both are supplied with the same length of wiring to the controllers and back. Both controllers are also the same.
We also noticed that after we switched off 1 pump when it was going very slowly, it failed to start again. You do know from experience that a pump draws more current to get it started that when it is running, so this could explain the failure to restart.
I don't know the answer. Could it be something to do with resistance in the circuits which in our case would include motor components, flow controllers, wiring and joins with strip connectors?