Re: 3 year old
When a body is sick it will cut down on spending energy in digesting food.
it sounds like that is what your 3 year old is doing.
I do not know what he is eating, but when you write that you don't eat refined foods, I get a picture of whole wheat, brown rice and things like that.
All complex carbohydrates are difficult for small children to digest at best of times. Some children do not digest them well until they get to the age of 6-7 (when an increased interest in vegetables also occurs in them).
The best foods for small children who do not digest complex carbs so well are breastmilk, meat, fish, and fruit (some fruit like hard apples should be minimized.) I learned this because my daughter had problems digesting. She lived on the above diet until 6 and was very healthy (=shiny hair and eyes, good skin, happy disposition, good muscle tone)
OR you can make the carbs are more accessable, for example sour-dough breads, or sprouted grains, or pre-chewed as they do in traditional cultures. good luck!