The dark circles under the eyes are food intolerance for my kids. When my daughter has a few drops of olive oil, she gets that. When she has rice, she gets that. Sometimes, when she used to have combinations of rice and soy, she would get very dark circles under her eyes that looked like she had two black eyes.
If you notice diarrhea in your son when he has milk, I wouldn't suggest putting milk back in then. He may be reacting to something else he's eating. I had to remove a lot more foods than just gluten and casein for both of my kids. Rice was a bad one for both of them. Soy was another very bad one. Bananas. Eggs. Avocados. Any kind of grains (millet, quinoa).
The list goes on and on. All these things gave my kids diarrhea, although the IgG said that they weren't really allergic to it -- but if they have constant diarrhea, of course they'll lose weight because food is passing too quickly through the system.