Sounds like something is draining the batteries/asking for more volts than what is available. Agreed if it was low charge, R&R unit should show the fault. I would try monitoring the voltage output while it is in emergency lower.

Potentially bad setting for emergency power as well, if my old memory of the MCE controller is correct, the controller does an initial boot up process, 30-45 seconds, before clipping the starter contacts as being available to run....sorta sounds like your timeline, so if on the query to get the starter ready, it finds no incoming three phase, restarts that whole cycle again like an initial power loss.