This is the classic example of why low-fat diets are disastrous for many people. When your body does not get the calories and fat that it needs, it begins to "slow down" so as to conserve it's energy. Any carbs you take in are immediately converted to fat for later use. Your body is essentially in "starvation mode." Your metabolism slows down and as you say, every calorie you take in seems to count double! Now when you give up on the diet and go back to your regular way of eating, you put all the weight back on and then some, because remember, your metabolism is now running slower. This is why so many people end up even heavier than they were before they started.
BTW, the human body does this as a defense mechanism against famine, something that human beings dealt with on a regular basis up until recent times. It is never a good idea to starve yourself on one of those low-fat diets.
What makes low-carb diets (such as Atkins) so successful is that you are not going hungry. Your body is satisfied and has no reason to panic and slow its metabolism down. If exercise is combined with the diet, your metabolism actually increases and you burn off fat even faster.