I have corresponded with many fellow autoimmune hypothyroid patients over the past four years and have read the testimonies of hundreds of others, in articles and on forums and message boards. What I hear from these patients, is something I have found to be true in my own case as an autoimmune hypothyroid patient (Hashimoto's Disease) and that is the fact that we can continue to experience mild to moderate symptoms, even while on optimal "thyroid hormone replacement medication" treatment. These symptoms can be intermittent or with some patients continual. The more fortunate patients rarely have symptoms while on treatment.

Surveys of thyroid patients on treatment have been conducted, the majority of the patients studied, being on the recommended optimal dose of thyroid hormone replacement medications and many taking natural T-4 and T-3 combo meds. The surveys had the respondents to report the effectiveness of their treatments and the results released in these studies, concluded that a majority of patients continued to experience a degree of symptoms.

As I continued to research this subject over the past several years, I found research articles by reputable medical research groups, stating that the disease process itself, caused by thyroid antibodies, called the TPO (thyroid peroxidase antibodies) and the TG (thyroglobulin antibodies), can also be a factor in causing symptoms. These research articles concluded that elevated levels of these antibodies can cause fibromyalgia type symptoms in persons with only sub-clinical hypothyroidism. Other articles stated that the autoimmune thyroid disease can have a degree of systemic (system wide) effect, so that the immune system response affects not only the thyroid area but other parts of the body as well.

Here is a one-sentence quote from one of those sources:
"However, a responsibility of the mechanisms involved in the autoimmunity rather than a direct action of thyroid hormones seems supported by the evidences that some rheumatic manifestations may occur even in euthyroid patients, or that they are more frequent in hypothyroid patient with autoimmune thyroiditis than in those without this disease."
(PubMed - Chronic autoimmune thyroiditis and rheumatic manifestations.)

This research article and many others, clearly attribute thyroid antibody levels to symptoms, apart from thyroid hormone levels.