Its impossible to diagnose via proxy, however some ideas:
The max 707 is a supervisor as you say, it will reset the chip if there is a reset input, or the vcc voltage to the chip is too low, or if the comparator section of the chip is under threshold.
It would stand to reason that either the processor supply is too low (have you measured it) or the comparator threshold is below the setpoint, I dont know what the comparator is looking at, it may just be battery voltage, the management may shut the engine down if the battery is too low, esp if the throttle is servo controlled or the cooling system is electric.
Your right about the eproms, Later ones dont need -5v, however I'm thinking your issue is power supply, or some run condition isnt met.
looks like battery voltage is 24v, are we talking a larger engine, mtu make some interesting motors.
I've had experience of diesels before, but only small stuff.