I agree, definitely have a Vet assess this situation, but make sure it is a vet who specializes in equine lameness. They are very keen on picking up things that we or others may not see.
For example, with Nelson's stifle issue, my regular vet did not pick up on him stabbing that leg slightly when at the trot, where my equine lameness specialist picked up on it when he watched Nelson moving.
I would get this checked out, to find out what is going on. I wouldn't be Eventing him until you get it figured out, because this could seriously hurt the both of you if he isn't clean over those solid fences.