I was diagnosed with Hashimoto's in 1997 or 1998 after having my child. (It's not uncommon to have an autoimmune issue pop up after pregnancy). Anyway I suggest you give yourself time to get the dosage right and adjust before reading too much into any continuing issues. It may take a while to get to normal.

I find with fluctuations in my weight (depending on hos much I am riding, etc.), I need to self adjust my dosage, but I've been doing this a while so I know what feels right. You need to get used to how you feel, get tested regularly and make sure things are normalizing.

I do ultra endurance rides with absolutely no problem now, and have for years. The thyroid is not an issue at all unless I gain weight and the dosage gets "behind".

Good luck.