Did you ever play the game charades in school? Or telephone? What people see and/or hear is NOT always what actually happened. Its like the movies where the kids overhear the parents being sarcastic, get mad becuase they don't understand its sarcasm, and don't stick around to hear the truth.
It seems to me that that is what's happened. Some busy body friend of the mom or their kid saw things and told their mom, etc... and that the ex is SO worried about what her social circle will think, and being politically correct that she would accuse your son and not believe him. It could be that there is a spiteful girl at your son's school that is trying to make him look bad for some reason. I mean what would you do if the daughter of a church member said something happened, you asked your son, and he denied it? If you believe your son, then the church member's daughter is a liar. You can't come out and say THAT, because then it make's the church member look bad. If that church member is someone who is friend's with people who matter to your social circle, then those people will be against you because you called their friend's kid a liar.
Your son knows the truth about his life. The fact that his mom puts her social standing above the truth is a sad thing for her. All it is doing is driving him away.
Good luck
M.