I havent grown an inch in two three years
you are doing everything right, you are not fat, you are at a healthy weight. because your body is still growing you will have a little extra weight. make sure to drink plenty of water keep hydrated. and you sound perfectly healthy, keep it up!
1000 calories isn't very much. If you're body doesn't have enough calories it goes into starvation & storage mode. This means that by not eating enough you're going to either keep your weight on or even gain weight. I suggest you eat at least another 200 calories, maybe more. What are you eating for lunch? Maybe you can add some nuts, boiled eggs, yogurt, or something else with a good amount of proteins and fats.