I think what happened in the time between your adding water to the pool and getting the SWCG up and running something tried to grow in your pool. Shocking with liquid chlorine is the best way to deal with this, your SWCG can only generate a certain amount per day and using the liquid chlorine saves on both cell run time and money.

Once this initial 'chlorine demand' is resolved, the SWCG should be able to take care of almost everything in the future