I was shocked to discover that my son had a peanut allergy that was causing his GI issues. What you describe sounds very similar to where we were when he was a toddler. I pushed for allergy testing (the RAST blood test) only because my daughter had an egg allergy that was not discovered until she was four. My son had similar eczema issues and had not been able to transition to cow's milk just like his sister. When we removed peanuts from his diet he had normal bowel movements for the first time in his life.
In 8 years of dealing with food intolerance issues, I have found that the medical community has not been much help. And my dh is a physician! While he is much more willing to look at food links now after two children with food sensitivities, food allergy as a GI response is just not something that has been considered a true allergy in medicine.
Even though my son has elevated levels on his RAST test, the allergist did a skin test and told us he does not have a peanut allergy since he did not have a response to peanut on the skin test. It is so frustrating to have a child that has explosive diarrhea if he eats peanuts, but to be blown off by the allergist.
There is still something in is diet that causes GI issues and I haven't yet figured out exactly what it is. I believe it to be soy (which is in EVERYTHING!!) but am also considering a gluten or wheat free trial. We repeated his RAST about 2 years later and most all of the foods are getting worse and yet again, allergist says no big deal???
Quite frustrating when you are the mom dealing with the poor child with an upset tummy and you can't get help from your pediatrician or allergist!! I have been looking into the GAPS diet (google will bring up lots of info) and have been considering going this route to see if we can finally clear up the GI and skin issues in our home.
I truly believe that the food (specifically processed) has much more impact on our health that we realize! Since we have converted to a whole foods diet and eliminated almost all processed food, our family has been much healthier. I never imagined I would be grinding my own wheat to make bread and driving 30 minutes to buy non-pasteurized milk but the benefits have been worth every bit of effort.