Nope, it's not, it's all about how your system is programmed, somebody with metabollic syndrome would tend to store fat not burn it. A calorie is not a calorie! Never was and never will be 
Context is everything with the 'calorie is a calorie' statement.
I've seen intelligent men battling it out for 20 pages, laying out their arguments for why it 'is' or 'isn't', without realising they are both talking about very different things.
The diversity in human bodies, digestive systems, endocrine systems and so on, is so great that the same meal might have a different outcome - even if we are just talking about calories in the context of energy.
However, even in that context, no matter how diverse the individuals are, strictly speaking 'a calorie will always be what it is' regardless.
Now, when folks start arguing the above two statements as if they were opposing points of view, that's when it gets ridiculous.