A starting dose of 100 mcgs is pretty powerful. Most doctors start at 50 and gradually taper up every few weeks from there. So it might be that if you were very hypo before meds, a sudden "surge" of thyroid hormone that you were missing before may have hit you harder than normal.
I had a very hard time starting on a dose of 75. Had so much joint and muscle pain, my GP ran a gigantic panel of tests looking for the whole gamut of arthritic and connective tissue diseases, all negative. But he's very ignorant about thyroid disease and probably hadn't a clue that meds can do that. The endo who prescribed it wasn't much help either. Eventually, it became clear I couldn't tolerate Synthroid and began taking Armour thyroid. I never got any side effects from it.
I don't know how much you've read about starting treatment, but it often doesn't go smoothly; not many people start taking that little pill and feel better immediately. Most will feel worse for a while and gradually improve as their optimum dose is neared. But as dea4 says, it could be an allergic reaction to that brand. You may do better with another, no matter what that doctor says.
Hope you begin feeling better soon!