Hey mcsolar, I run too. Calorie burn calculators seem to vary wildly. The one here says I burn almost 1000 calories for 5 miles (!) whereas I just compared on a couple of running sites and got 530 and 457. The rest of their calculation (for everyday activities) also seems high, though not outlandish.
I find the food calories here to be enormously helpful and, I think, pretty accurate, but I don't lose weight eating as much as it tells me to. But I would bet that it's closer for some than others; everyone's body composition, metabolism, etc. is a little bit different. I wonder how good it is at adjusting for sex, age, weight, etc.
I guess the point is to experiment and find what balance works for you, and to be aware that if the weight on the scale isn't corresponding to the calculators here, the calorie burn formula might be a more likely culprit than you doing something wrong or something being wrong with your body.