My experience w/this was a horse with dental issues.
She had very sharp points in the cheeks along her back molars. When the halter was put on her, it pressed the raw spots (she had them from chewing) into the halter cheekpieces and hurt her. Same as when pressure was applied for leading her, she would rear and shake her head.
What we did was use a neck strap for leading her around til we could get her looked at by a dentist.
It is often hard to see these b/c the cheeks sort of press around the back and they are very far back there, but this may be your stallion's problem.
If there is nothing physically wrong w/him, I think you need to look at the fit of the halter as well as inspect where it sits.
My otherwise calm stallion would freak out if the harness he was wearing touched the backs of his ears (he had nothing wrong w/them, he was sensitive there). We had to find a longer browband to keep the straps over the poll from touching his ears at any time. Could be your halter is touching him at the base/back of his ears even if there's no inflammation or cause for discomfort, it may just be that he's sensitive about it.
Good luck w/your detective work and please do let us know what you find, if anything.
Liz M.