Other replies are good guesses as well, but I agree that there could be some stiffness, which is causing pain to that side. Try some flexing exercises from the ground. Once in the saddle, ask for the flex to stretch him out before working. HTH.
Buy a tiedown. I don't Like The Idea Of Tie Downs But My Horse Had The Same Problem And so I Bought A Tiedown And Put it Really Loose So She could hold her head like normal and stretch out and whatever and It Worked Great And Then A Few Months Later When She Stopped Trying Too Toss Her Head I Took It Off And She Never Did it Again