Jumping in late to this but all my DD's are MPI (DD2 was dairy free until 5 years old). Intolerances have less acute symptoms than an allergy - gut/bowel issues, ezcema, sometimes behavioural and may take longer to show up where an allergy would be fairly quick - hives, vomitting, swelling etc.
Poor C, sounds rough on his bottom! DD2 always had severe constipation from dairy but DD1 & 3 tended toward loose/mucousy stools and all 3 had ezcema.