How long have you owned him? If he is new to you and continues on with this, I would highly suggest getting him scoped. Of course it could be anything, could just be out of shape etc. But from my own personal experience of purchasing a horse that would breathe heavy and nostrils flaring, a scope is the only way you are going to know whats happening. Im not sure I would suggest working him harder to get him used to the work until you have some definate answers. You would feel terrible if you worked a horse hard that truly couldnt get enough air.