LA batteries with a shorted cell can heat up to the point of exploding--steaming sulfuric acid could quickly lead to a disaster. Stop all charging on the batteries until they cool down and only then go near them. If the battery is shorted and/or the alternator is over charging them free hydrogen gas will be released with the "steam" and any ignition source will cause an explosion.
From what you describe, you may be only a spark away from a life threatening disaster!
Jack