Went back and reread your post. I forgot about the reflux part---yes, babies who have a food sensitivity are often misdiagnosed with reflux, so that makes the possiblity of a food sensitivity even more likely. Does he have any signs on his skin, such as eczema or frequent diaper rash? That can be another sign.
Just wanted to mention too, that oftentimes babies have an intolerance to foods but not a true allergy. My babies have had intolerances to many foods and thankfully outgrew them in their second year! So, even if it is a food such as dairy (wheat, soy, corn are other common ones), it doesn't necessarily mean it is an allergy that will stick around, thank goodness!