Hashimoto's Thyroiditis is an autoimmune disorder. My body is attacking itself. Taking synthroid helps to stop or lessen the autommune response. In theory, it could continue to be attacked by my own anti-bodies. Time will tell. The thyroid medication did not cause this.
Say what you want, I will continue w/ my hormone replacement (which is a natural hormone, not a man made drug.) I was toughing it out for years - eating right, taking supplemets (yes, omega 3 omega 6). It took me awhile to get to this spot to feel that taking it is ok. The fact that I am not feeling like I want to jump off a bridge is enough evidence for me.
As far as physical symptoms related to running, I have felt similar problems that the previous poster. Feeling flat, difficulties w/leg lift, and hamstring problems that came up (I had never had any muscle problems in the past). Overall sluggishness. I would feel great one day, then very flat and slow the next. I was training a lot, and not losing any weight.
On the synthroid, I have more days w/ a spring in my step and recovery seems quicker. I have more energy as well. Getting off the couch is not a problem.