Not sure what type of "3-stage" charger that you use, but both my stand-alone 3-stage charger and the one built in to the trailer converter are automatic. In other words, once connected to the battery, the charger determines the initial rate of charge based upon the state of the battery, and charges to 100% (or near to it) depending on battery condition. It will then go to a "float" charge where it can be left indefinitely connected. With my stand alone charger, if the charger has been pulsing and charging for 24 hours continously without reaching 100% state of charge, the charger discontinues charging and indicates a battery that is non-rechargeable. Incidentally, my stand-alone 3-stage charge is designed to be connected to one battery only at a time .If yours is the same, perhaps you were attempting to charge both your batteries at once and your charger couldn't handle both ???
Just my thoughts on your problem.