This is likely related to a lack of digestive enzymes and/or bacterial flora in his digestive system. You need to supplement his diet with a non-dairy probiotic supplement. Do that for 2-3 weeks and see how it goes, it should improve fairly quickly. Because he already has allergies, it's particularly important that he doesn't consume a lot of processed/packaged foods, because otherwise you might soon find there is n increase in the number of food allergies.
Also, please consider NAET, it's a non-invasive technique to eliminate allergies without drugs.
Best of luck.