My mare used to to this and was also a headshaker. Backed too young and pushed too hard by an apparantly! reputable professional. It becomes habitual and cannot be cured.
Could be teething, his front teeth will be coming through about now, not the 2 right in the middle as they should already be adult ones, but the next pair along. On my 3 year old you can clearly see them under the gum line pushing to come out!