Sometimes a battery gets run down so low that the charger won't recognize it as a battery, and won't begin to charge it. If the battery is just run down and not faulty, you can still recharge it with this method.
Just connect jumpers from the discharged battery to a good battery, then connect the charger to either battery.
The charger will recognize the battery (batteries) and begin charging. Once the charger shows a partial charge, you can disconnect the jumper cables and just charge the bad battery.