I find the calorie burned estimates on here quite high, by about 50% for me (it says I burn 3000 calories most days and I know it's more like 2000). That goes for both their general lifestyle calculations and most of the individual activities. I would guess that you're not seeing any loss because you're actually only burning about 2000 calories.
That being said, if you want to gain weight, even lean mass, it's not going to happen on a calorie deficit. So it might be better to keep eating around 2000 calories, make sure to get enough protein, and stick with your workouts. Give it some more time and if you don't see results, maybe add more resistance training and/or vary your workouts more. With any luck, you'll gain muscle mass without increasing fat, thus decreasing your body fat %. It doesn't sound like you have much fat to lose, so cutting too many calories might cause you to lose lean mass as well as fat, not what you want.
If you've only been working out and tracking your diet for a few weeks, it may just take more time to see results. Good luck!