Your Naturpathic doc may have done an Intolerance testing. Babies who have MSPI, milk/soy protein intolerance, will not show up as having an allergy to dairy when an allergy test is done, unless of course they are allergic. My son, for example, tested fine for dairy and soy in the skin prick test, and the rast (blood work). However he was on Neocate, a special formula, because he was intolerant, it made him have bad eczema, constant runny nose, itchiness, etc. So one can have an intolerance to something without being allergic, as an allergy affects the immune system, and the intolerance does not. The symptoms can be very similar, except with an allergy they may go into anaphylactic shock, whereas in an intolerance they would not.
May I ask what kind of symptoms your son had to these foods?