Yes, this is possible! Allergies/sensitivities to foods can affect any body system, so there may be more inflammation and irritation going on than just the vomiting, and I wish so badly that I'd known more when my younger child was very young. Also, lactose intolerance would not show up as an allergy as it is an inability to digest the sugar - lactose, as opposed to reacting to the milk protein - casein.
The allergist did not help!!!! They only help if it is an IgE food allergy and not for an IgG or IgA food allergy! My allergist could not figure out my HIVES, and I only did after my kids had to get off gluten and dairy (in fact, one is so sensitive she eventually had to get off all standard grains). See here: http://www.foodsensitivityjournal.com/2011/03/its-not-men...
I strongly suggest Dr. Doris Rapp's book "Is this Your Child" even if the foods are not affecting brain function, as she has a lot of useful ideas and what to do about it. (See that website: http://www.DrRapp.com/ and the book 'It's Not Mental' - http://www.ItsNotMental.com - for what can happen in the long run).
Here is something to keep in mind with a food elimination trial:
1 - One nurse told me she saw one patient still reacting to a food (hives in that case) for FOUR weeks after the food was discontinued, so you need to do it long enough.
2- There can be multiple foods being reacted to.
And lastly, you may need to take measures to heal his gut (http://itsnotmental.blogspot.com/2011/03/gut-brain-and-ba...)