[corty]

No, all calories are not the same. The basic process for measurements is "burn it, measure the energy output". " Burning" as in "gas flame, high heat, oxygenated atmosphere". This is something your body doesn't do, even if you supposedly "burn" calories. Your body uses different reactions that are often less efficient, meaning the energy output will be different from the calories measured. Nowadays some of those errors are corrected for, but not all of them. And depending on your personal metabolism, from genetics, daily changes and nutrient status, your body will be less or more efficient with some foods.

[AnIdiotOnTheNet]

Irrelevant. If your body extracts only 50Cal from a 100Cal cube of sugar, but you counted that 100Cal value against your daily limit, then you're still achieving your goal. The problem is often that people set too high a limit and overestimate how much they burn during exercise.