does it only show up when he eats?
my daughter is allergic to all the johnsons baby products, she had a rash that came and went, so we switched to aveeno. her pedi said alot of babies have issues with bath products.
another formula you could try is enfamil nutramigen, its for babies with milk protien allergies. also, alot of babies who are allergic to milk protiens are also allergic to soy protiens.
http://www.enfamil.com/app/iwp/Content4NoBlurb.do?dm=enf&id=/Consumer_Home/Products/Family_of_Formulas/Nutramigen_LIPIL&iwpst=B2C&ls=0&csred=1