My daughter also has peanut allergies and it has been a nightmare for us. She is 2 years old and I have already had to administer the EPI-Pen twice.
My allergist has told me that she is the highest level (airborne allergic) and we have to be extra careful with her and what she is around.
Last month when we were at the allergist I asked the question about the statements they put on the back of products "Processed in a plant that processes peanuts...." and what that meant for my daughter. She said the manufacturers put that on the product to cover themselves and that it is really not a concern. She reccommends that we test my daughter every year for new allergies. She has developed allerigies to cats, dog and now soy, and the allergy to peanuts has increased to airborne/life threatening.
My advice to you is that you have him tested again as it may be that he has developed an allergy to soy, milk or whey. Which would make sense in your situation.
Hope it helps!