The eye problems are likely not directly related to your thyroid problems or the replacement hormones you are taking. They sound like they are caused by Graves Eye Disease (also known as Thyroid Eye Disease) which is caused by different anti-bodies than the ones that caused your Graves Thyroid Disease. These antibodies cause a fat-like substance to be deposited in the muscles behind the eyes, which eventually push the eye out of the socket, causing the characteristic stare. Somehow they eye movement also causes the lid retraction you are referring to.
The antibodies can be blood tested for, I believe. I'd say at this point you should be seen by a good ophthalmologist who treats patients with GED. Your endo should be able to refer you to someone, I would think.
I'd advise to make sure you are seen soon. Even if your eye problems don't progress any further, it is better to be safe than sorry. Sometimes GED progresses until it causes double vision and in rare instances, threatens the optical nerve. Good luck to you.
Have you had your antibodies checked again?