I honestly don't know if this will be of help, but with some of the health history you mentioned for both you and your little one, I figured it at least wouldn't hurt! Some of this may be something you already know, so apologies if it's not useful. :-)
There might be a possibility that the low levels of allergens you come into contact with may be enough to affect your child, if he is extremely sensitive to gluten, or the dairy, etc... Have you investigated a lot of the processing and/or farming in your food supply and other products? Or joined any groups that keep any lists of products and places the allergen might be found?
My family has numerous issues with various foods as well, with an extreme sensitivity to a few of them. With this high sensitivity, we were remaining sick and couldn't figure out why until we got some help from some folks on the internet with the same issue who helped us find safe foods. http://www.glutenzap.com/forum/index.php is one that's good for super-sensitive celiacs, which helped me ferret out many sources of gluten cc in my diet that I'd never even thought of before, but I don't know of a good place for super-sensitive dairy or soy allergies, I'm afraid.
Examples of some of the crazy places we've run into allergies:
1. A wax that is frequently used on organic apples and citrus (shellac or lac wax, based on an insect) has soy or casein added to it for texture. Even cutting off the peel hasn't worked for us, because enough sticks to the knife as it cuts through that it contaminates the inside flesh and made us sick. Some other fruits may use this too, but I'm not certain, but many waxes and coatings have various ingredients that could be an issue.
2. Maple syrup - all in the USA are required to have a defoamer added that is rarely listed on the label. I found a small, local maple syrup that was using half-n-half as their defoaming agent without adding the required dairy warning to their label. :-(
3. Wheat was used in some of the glue-type agents in some older particle board products so can be a touching hazard for those with wheat allergies.
4. A locust/grasshopper pest killer called nosema locustae is sprayed on wheat bran and sprinkled all over the vegetable field and the produce - for something like, say, broccoli, it can be impossible to completely wash off. It can be used on both organic and conventional fields, depending on the brand.
These are not levels of contaminants that are enough to make many people react. However, for those who are extremely sensitive, they can still cause a reaction. A celiac friend of mine with a breast-fed 12 week old has had her baby react twice already, really badly, to gluten levels that didn't bother the mom. She's had to alter her diet to be even more gluten free than usual, now.
Re: gluten. Gluten free food actually has gluten allowed in it, even though the amount is very low (you probably already knew that, yeah?). However, in studies, they've found that some people react to low enough levels of gluten that they WILL react to the gluten levels allowed in GF food. The FDA in the USA even mentioned in their huge, 96 page assessment on the safety of gluten and gluten free food that if they were going to create a safety standard that would make food safe for everybody, even the really sensitive ones, they would have to have a <1 ppm standard. Most gluten free food allows 20 ppm.
Two celiacs in my family need <5 ppm of gluten or we stay sick. Avoiding this level of gluten has required more research to figure out than avoiding our other allergens. Some examples: many farms use mulch that has gluten containing straw on it that can contaminate produce (like some brands of strawberries and some types of mushrooms) and may not be able to be washed off. Some soaps and rinse-aids to wash our dishes in the dishwasher tested positive at over 5 ppm (I tested some, and some acquaintances also tested some). They've also recently discovered that gluten tests that are usually used to determine if foods are gluten free are underestimating gluten levels in foods with hydrolyzed gluten, such as GF soy sauce.
If your little boy is extremely sensitive, these types of things might be enough to make him quite ill, yeah? One of the reasons that the gluten occurred to me was the similarity in symptoms for your little one and some children I know of who get gluten cc. The constipation was a big one, along with the eczema. But also the pseudo obstruction rang a bell. I know of two celiacs, one adult and one child, who have an intussusception as their reaction to gluten. It just seemed to me that if this could be caused by gluten, perhaps a pseudo obstruction could be, too.
EDIT: also, the getting sick when the little one had the contrast, too, made me think of this possibility - I had that as well and I was SO sick off of it! Many medications are terrible at testing for gluten and other allergens, if they test at all. However, if your little one was very ill after having the contrast, you might want to get the manufacturer name of the constrast and find out every ingredient in it - it might help narrow down a possibility for any substances that are an issue, you know? If you haven't already done that, that is.
Just a wild shot in the dark, from someone with no medical background, but again, I figured it wouldn't hurt to share as the only way to test it would simply be for you to examine your diet and do some research, you know?
Very much hope that you are able to find the answer soon. So awful when our babies are sick and we haven't discovered the reason yet. :-(
Edited by Shaunamom - 4/17/12 at 12:42am