My own experience seems to demonstrate that calories DO matter.
I've recently reduced my carb intake quite substantially (although I'm not low-carbing by any means) and over the last two years managed to lose 5 stone. I'm now attempting to maintain my weight and so have introduced additional nuts and seeds to increase my calorie intake without going back to the major post meal blood sugar spikes I used to have on a high carb diet.
I managed to gain 2 kg over Christmas, and another 2 kg while on holiday, so have recently been trying to lose again, without much success. I decided to count calories on a good day, and found I was simply eating too many, and the biggest single source of calories was the nuts and seeds I was eating.
I have now cut in half the amount of seeds (ground flaxseeds on breakfast, whole seeds on salad at lunch) I'm eating, and hey presto, in the last two weeks the weight has begun to drop off again!