What Causes Weight Gain Despite Taking Synthyroid?

I take .88 Synthroid daily. I gain approx. 3-4 lbs. every 2 months resulting in a 30-35 lb. Weight gain overall. I eat about 1300 calories a day. I just started a boot camp exercise program. I am so afraid I will have a weight gain even while exercising. Is this what I have to look forward to for the rest of my life? Eating like a bird and exercising only to gain more weight. My doctor says "my numbers are fine...." Very frustrated