The FitDay resting metabolic rate calculations can be way off, so that could be part of it, but by far the most likely explanation is that you are not measuring your food, and your belief about what a "serving size" consists of is much larger than what the product label says.
I remember the first time I weighed out what a single serving of my favorite cereal was, I was shocked! Get yourself a food scale, and weigh everything.
What I did a few years ago was to keep careful records of my weight and all my food intake and exercise. I fit a regression line to it, and found that I burned about 1740 kcal/day (which varies some with body mass), but this was several hundred calories less than was calculated by FitDay.
I don't know of anyone else who has taken the time to really tally up careful records to determine their RMR... if anyone else is out there, I'd be interested to hear what your experience was. But once you do it, then if you keep careful records of your food intake, you can measure your weight more accurately with your food log than with your bathroom scale.