I would think that it is the body healthfully ridding itself of whatever toxin or pathogen has been bothering. I don't know what your son has, but if it is autism then the gut needs to be cleaned out. A lot of the live viruses/bacteria in vaccines end up proliferating in the gut, especially in the gut of those who then become plagued with autism, autism spectrum disorders, ADHD, Allergies, Asthma, etc. I

f your son is eating so healthy and now he has diarea I would take it as a good sign. I was on Miracle-Mineral-Supplement and got diarea after a recent dose and now feel better than ever, it really gets the pathogens out. So please check into Miracle-Mineral-Supplement which also oxidizes mercury and metals that can cause autism. Start with a very small dose. To help autism I would detox the brain of metals and the gut of organic pathogens such as viruses, bacteria, fungus, yeast, which are all parasites by the way, living off of people and when out of check produces symptoms.

Don't forget super high doses of friendly flora such as http://www.customprobiotics.com
offers which can help reverse autism especially if administered before the sixth year of life. Zeolite and terramin clay also bind to toxins in the gut and body and are very natural, they are available at http://www.i-amperfectlyhealthy.com
and other websites. My kids love to drink the "mud" that we make with the terramin clay, it also alkalinizes the body.

Your son is so blessed to have such a parent as you to who is looking into alternative cures and using a holistic approach.