err... I'll try to explain. Glycogen is what your body usually burns first for fuel, before using fat. Your body stores a lot of glycogen (7 - 10lb) which is why people have such a dramatic weight loss in their first week. By following SS which is low carb, your glycogen stores do not refill.
When you start working through the plans, and reintroducing carbs to your diet, the glycogen stores start to refill, but you dont gain weight as you are still taking in very few calories. By the time you have finished working through the plans you are back to a "normal" carb intake, and normal glycogen levels.
I Hope that makes sense. As I said, Im sure a CDC will be along soon to give you some proper advice.