It's usually hind limb pain (hocks usually) or back pain (which is most often caused by hindlimb pain). Get the vet to do a lameness check and poss a referal to a good physio.
One of mine does this, turns out that he has torn a muscle in his hind quarters so he is now having treatment to re stimulate and repair the muscle. Also because the muscle is so tight it is pulling his pelvis out. So once the muscle is sorted i can get the backman out to do his pelvis. Darn horses.
My mare has done this for the nine years of history that I know about her.
When I had her she used to do it all the time, now she only does it in trot and it's only noticeable on the roads as you hear the extra tap in the stride.
Had a full lameness work up and the vet could neither cure it with blocking, or make it worse with flexion tests etc.
He concluded it's largely mechanical and of no detriment to her. Keeping my mare fit and lean does seem to help. The more work she's in, the better it is.
I've given up wishing to cure it and have finally learned to accept it's just her way of going.
I have shod a ouple of horses that do this. One was a conformational fault. The other three were all ridden by the same rider (and one was new and not long after he arrived he started doing it too) and i believe it was rider error (or pain) somewhere.
Also those horses were pointers so didnt get schooled. The rider had a bad knee.
It is worth geting the back and body looked at, if that shows nothing and its not conformational then perhaps the horse is not engaging its hind quarters.