I think your experience illustrates the fallacy behind the whole "calories in/calories out" equation we've been told. It's just not that simple. Sure, you put a certain amount of gas in a car and each car will go a varying amount of distance, but people don't work that way.

The body is a whole complex interaction that goes way beyond mere calories. In my case, eating Atkins made my calories go UP and my weight went DOWN.

However, the composition of my diet radically changed. I went from eating 70% carb/10% protein/20% fat to 70% fat, 25% protein, and 5% carb.

In this case the science you are trying to apply to yourself is simply wrong. You must look elsewhere for the solution. For me it wasn't calories, since mine went up. It wasn't exercise, since my level didn't change before and after. But my diet COMPOSITION was, in my case, crucial.