Are you entering the calories you burn during your workout into my fitness pal? There should be something you can click on that says track exercise. Once you put your exercise for the day in it will automatically adjust the calories you can eat for the day to reflect this. Mine will normally say around 1300 too, but since I know I will do about a 500 calorie workout I will typically plan to eat around 1800, even if I am not working out until later in the day.