Did he look anything like this?
That is my mare. The vet couldn't figure it out either. We tried injecting her stifles and it didn't help. Either she has soft tissue damage to her stifles or arthritic hocks or something in her back/hip. (X rays showed very minor arthritis started. She is only 8 yrs old).
I am planning on getting a second opinion. She also trots sound and only has issues at the canter. She injured her stifles as a 2 yr old. I think this is related to that and only now becoming apparent. Or it could be unrelated.
Your horse probably does have something wrong with him. My mare flexes sound unless you modify the flexion (hold the foot back like the farrier does and flex it up that way). Wish I could explain it better. It is not the regular flexion where you hold the foot more forward to flex the hock. It does explain why she is bad for the farrier with her back feet. Our farrier is very understanding at least!