It is, indeed, hard for a single program to account for all of the variables each of us bring to a work out. I have a couple of sources of calorie burn for various activities. In some cases FitDay underestimates, in others it over estimates. Since running is my main thing and I have a Garmin Forerunner that I have a lot of experience with, I tend to adjust the FitDay calculations to match whatever the Forerunner says.
Otherwise I am totally in agreement with Almeeker - if at the end of the week all the fancy-schmancy Fitday calculations say you should have lost weight and you didn't... adjust how you use the calculations. For the most part as long as you are honest, the calories you eat are correct, so it is the calories you expend that needs to change.