I had carpal tunnel syndrome when hypo, which resolved once on meds and has never returned. Tarsal tunnel syndrome is the corresponding syndrome in the ankle, so it could well be thyroid related.
Please post current thyroid blood results with reference ranges (they vary lab to lab and have to come from your own report), and as Kristina suggested, give us a brief meds history.
Muscle pain can be attributed to thyroid conditions. Are you on medication for Hashimotos? My doctor started saying 'carpal tunnel' syndrome to me at one stage when I was hyper and I dismissed it (correctly). Do you have copies of your thyroid blood tests?