Sounds more like a saddle problem if this is a western saddle than a pad problem but hard to say with out seeing a picture.
One cause if it is a saddle problem will be with how the skirts are fitted during construction of the saddle. Are the skirts on your saddle laced together at the back right to the point of the skirts? If they are and the skirts were not blocked/fitted properly around the back point of the bar the skirts could be bowed down slightly and it could be the skirts are rubbing on his back. Its kind of hard to explain without some pictures. If your skirts are laced right to the end then you could just unlace them back a few inches which would allow the skirts to flex upward some and see if that helps your problem at all.
If its an english saddle then I don't have the foggiest idea what could be causing your problems!