I have hypothyroidism as well. Random aches/pains are normal but always double check with your doctor. I was diagnosed 6 years ago. It comes with the disorder.
It could mean that your thyroid function is lessening all the time. Do you know if you have Hashi's? As the antibodies attack the thyroid, it becomes less and less able to produce hormones (this can happen no matter if you have Hashi.s or not, but it's just about a sure thing with Hashi's). So, you have to retest regularly and adjust your dose accordingly until the condition stabilizes (your thyroid "dies" and you're on a full replacement dose).
If I were you, I'd call jy doctor and ask him to order FT3, FT4 and TSH. You need all three. TSH is not adequate for managing meds.
How much Synthroid do you take? Any other symptoms returning?