I had a 1999 Ford Ranger that would not start if the mounted battery was dead. I tried jump starting with my other vehicle and nothing would happen. I unhooked the dead battery, and the truck started right up. I contacted the local Ford stealership and they said that the truck could tell that the mounted battery was dead. It didn't make sense to me, but, I am not an engineer.
Had the friend call me and had the same problem. He unhooked the dead battery and it started.
I have a couple of smart chargers and if the charge is low enough, they will not work. I also keep a stupid charger on hand to start the process.