[Mark McLeod]

I certainly disagree about the purpose of the backup battery.
It only saves the robot from rebooting in the middle of a match when the robot main battery voltage dips. Something that doesn't matter in demo presentations. We use the old controllers constantly and have never included the backup batteries.

That would have been a really bad band-aid if it was to solve a runaway robot problem (from a different generation of control system). It would be a very high risk solution to depend on teams running with a charged backup battery if they couldn't be depended on to run with a charged main battery either.
Estop plays no part. That only works in any case if the robot controller from any generation is listening and responsive.
I do know ways to accidentally power the speed controllers while the Basic Stamp RC from that generation is disabled, but I'd lean towards a corrupted Master controller program allowing that to happen. Which could have been caused by low voltage, but the solution is a circuit/master code redesign.