You can run a pump with it unplugged? Congratulations, you've got the world's first successful perpetual motion machine .When I hooked the pumps to my truck battery and unplugged the pumps, the LED lit up solid but only one of the pumps ran.
Seriously though, if only one pump runs on battery I'd double-check the FPPMk2 circuit connections; also try isolating the other pump and its PDM and then try running them from battery alone. Maybe that pump is reluctant to start up at 12V?
Did you mean with the two old PS plugged in and switched on?But with the pumps plugged in, the red LED flickered.