I haven't been diagnosed with Fibromyalgia, but am quite certain I suffer from it. I have been diagnosed with Hashimotos auto-immune diseasewhich is attacking my thryoid. I will venture to say YES that hormonal supplements DO affect the very interconnected endocrine system. Our bodies are a whole system, not a bunch of non-related parts. I was given a prescription for Levoxyl the first month I took medication. For me, it was an AWFUL experience! Within a week I was suffering from parathesia (pins & needles) and skin crawling, insomnia, misery! I went to the endo and she didn't care! Said it was NOT the drug. Although she liked the fact that my TSH went from 7.56 down to .4. For doctors its often allabout the numbers - to hell with your symptoms! She is now my EX endo after only 2 visits. I had my primary care doc prescribe Armour, and it has made a big difference. I didn't take HRT after my hysterectomy & ovary removal 12 years ago. From what I have read, estrogen dominance can affect the effectiveness of thyroid meds. I also believe (myself) that only a T4/T3 combo can truly mimic a functioning thyroid that is either missing, not working or attacked by Hashimotos. I read that most fibro patients have some type of thyroid problem, most often Hashis even if their blood work fails to show high levels of the antibodies.
From what I have read, if I were you I would be looking into bio-identicl hormone therapy if you are taking synthetic hormones and I would also be looking at natural desiccated thyroid.