If the changer can only charge in pairs, then there is no way to handle unbalanced cells (one half-empty and the other completely empty, for example). In this particular case, the Sanyo MQN06 charger will stop charging when the first cell is full. So the other one is still only half-full.
Most other cheaply-built chargers will only stop charging when both cells are full. But that means the first cell will be over-charged by 50%. This is bad for battery lifespan in the long run.