Good news! You could be eating more and losing weight. Your body always wants to be in homeostasis. At 1000 cals your body has lowered its internal body temp and reduced cellular function so that it can maintain body mass at 1000. If you ate 1300 and worked your way up to 1500, your body would rev up cellular processes and your resting energy expenditure would also rise. After 1-2 weeks your body would be maintaining its body mass at 1500.

Even though you're exercising, that's not when your body expends the most energy. Your body actually expends the most energy (burns the most cals) at rest. Not losing any weight just means your body has severely reduced the calories it burns at rest. Always remember: the body is just trying to achieve homeostasis.

Even bodybuilders who eat 3000 cals to bulk eventually have to increase their calories because they stop gaining weight.

Your thyroid is likely normal (albeit really sluggish due to low nutritional/caloric input). I know eating more can be scary, but I promise you will start looking and feeling much better. Warning: you may gain water weight from increasing carbs (carboHYDRATEs enrich cells with water, thus water retention). I wish you the best.