What you're seeing is the amount of charge you're putting in the pack. The batteries are not at zero capacity to begin with, there is still some juice in them, this is typical (Critical in lipos!). When you start a charge, the charger starts at zero and charges by watching the rate the batteries take current. As the battery gets close to it's capacity less and less current is drawn. When this gets low enough and there is little change the charger "knows" the battery is full. It's a little more complicated that my description but you get the idea.