has he been checked for laminitis? some native ponies are prone to this if their keep is too good . if you can rule this out, is he unshod but doing work on hard ground - if so shoe (at least on the front) and maybe with leather pads to protect the sole - your farrier should be able to advise on this. does he have flat soles in which case it could be bruising, specially if he's been over rough ground - I'd check out any medical or exercise related reasons for the lameness and chat with vet and farrier. he could be footsore for lots of reasons. good luck and keep us posted.