I think I sort of figured out what's going on with it not shutting off. I switched back to conduits and a structure pipe with the gate on the cell. It seems that sometimes the cell never actually fills up. It will sit bouncing around just a shade below 600,000MJ, but never actually hitting 600,000. As soon as I broke out one of the conduits on the sending side, it filled up and shut the engines down as intended. The odd thing is the engines are making a lot more energy than it being drawn out, so I don't get why it never actually touches full.