Figuring points and calories is not an exact science. Besides, how we burn calories also varies depending on what we are doing, the temperature, etc. When I was in DC, we had a phrase: "Good enough for government work." What this meant was you did a good enough job to satisfy the requirements, but did not overexert effort or waste resources trying for "perfect." I think this applies to our weightloss efforts also. It is not the extra points of protein or fruit that is going to do you in, it is those extra cookies! So try and be strict when figuring out the points for sweets etc that are not "necessary" and don't sweat as much the points for things that are good for you.
My opinion, anyway.