I know little or nothing about food intolerance syndromes. The google search I just did on "food intolerance" and "vaccine" revealed that some of the same shaky and unscientific studies that try to link vaccines with autism are attempting to link vaccines to bowel diseases. Before you take any such claims seriously, you have to consider that autism and bowel diseases strike unimmunized kids, and the vast overwhelming number of immunized kids are perfectly healthy. No credible data exists showing any causal relationships between vaccines and autism or bowel disease. But do the searches yourself. Confront your doctor with any credible looking data you may find. But don't, please don't, trust anonymous tips on the internet where the life of your child is concerned.
Well, duh.