In a recent lecture by Dr. Paul Cheney, he states why he believes it is not a good idea to treat with thyroid hormone for ME/CFS. See from 22:00 to 25:50 in this video. In short, he believes that the brain responds to ME/CFS by intentionally down-regulating thyroid, forcing the body into a low metabolic rate. This is because the body 'knows' that it has lost the ability to deal with oxidative stress. Therefore, the body shifts into a low metabolic state in order to create less oxidation, a measure which Dr. Cheney describes as literally "life-saving." I believe he is referring to the tendency of oxidation to lead to cancer, but I could be wrong about this.
Dr. Cheney states that he can tell if someone truly needs thyroid supplementation by their blood TSH level. TSH is Thyroid Stimulating Hormone--the chemical signal that the brain (the pituitary to be exact) sends to the thyroid gland telling it to produce more thyroid hormone. Dr. Cheney says that people who are "true" hypothyroid cases actually have high TSH levels, suggesting that the brain recognizes the need for more thyroid hormone and is sending the signal stronger (but for whatever reason, the message isn't being received.)
In ME/CFS patients, on the other hand, TSH is usually low (mine is) suggesting that the patient's low thyroid function is 'intentional' on the part of the pituitary. *I did some liberal paraphrasing here, but I think it's an accurate summary of Dr. Cheney's views.
You can imagine my concern given than I have been taking thyroid supplementation on the recommendation of one of my ME/CFS doctors, since January, 2012. There's no question that it has made me feel better and has certainly improved by low body temperature issues (although it hasn't solved them completely). Now I don't know who to believe and I have a difficult decision to make. Coming down off of thyroid hormones will not be fun. I need to do a little more research and ask for more opinions, but I know which way I'm leaning.
*Thanks to the excellent blog CFS Patient Advocate, which is where I found the Cheney video linked above.