have him try shooting both eyes open and focus on the TARGET not the pin. look THROUGH the peep and focus on the target. the pin will be there and not as clear becasue it wont be the object your focused on. put it where you want it and send the arrow there. i have an asigmatism and wear contacts. i found that was the best way for me to shoot. my shooting improved alot...in hunting conditions if i close 1 eye and try to shoot i cant see because my peep gets all wierd looking...pretty sure its from the asigmatism. if i have my anchor points right and can see my target and pin, i have to be looking through the peep when shooting both eyes open so i dont have any worries.

going to local 3d shoots and shooting alot in the dark woods helped me learn that...

good luck with your son. surely gotta be a method or something out there that will help...sounds to me like hes focusing on the peep or pin and not the target.