I recently had lots of different joints that were aching. My endo didn't have any answers for me, although he did test me for RA and that came up negative (luckily!).
But when I recently had arthroscopic knee surgery the orthopedic surgeon detected "calcium crystals" in my knee. When it was sent to the lab it came back as being CPPD (Calcium Pyrophosphade Dehydrate) deposition disease. Basically, the way it was explained to me was, people with endocrine system disorders (I'm also hypothyroid), have a higher chance of developing these crystals in joints. They seem to have no idea what causes them to happen though.
There's nothing that can be done other than taking over the counter arthritis med (like tylenol, etc).
The crystals in my knee got scraped out during the surgery and since then that knee hasn't hurt a bit. Problem is, some of my other joints still hurt.
I wonder if it could be the same thing with you?