Plain and simple: you're not absorbing properly your food. You're very likely to have a condition named leaky gut, which could very well be the cause for your hypothyroidism and your adrenal fatigue. This means your digestive system is not working properly, the root cause being an unbalanced gut flora.
May I ask how is your digestion? Any discomfort? Fatigue after meals? Bloating? Constipation/diarrhea?