You say he doesn't drink any juice. So are his fluids only water and milk? Any juice-flavored "drinks" or beverages? Does he get any diet or sugarless products, like sugar-free treats or drinks, sweetened with anything ending in "itol", such as sorbitol, xylitol, mannitol, erythritol?
I'd have him see a pediatric nutritionist. And in the meantime, there's a fairly simple, harmless thing you can try, especially since you say you feed him fruits and vegetables. Try eliminating all products containing apples, cherries, pears, and red or purple grapes. That includes any drinks containing any of those products, or the fruits themselves, or any applesauce, etc. And check the multivitamin and the probiotic labels too, for any apple, red/purple grape, cherry, pear, artificial sweeteners, anything ending in "itol".
Those fruits are natural sources of sorbitol, and in some children (and adults) sorbitol can produce some pretty uncomfortable digestive results. My daughter had a similar problem at that age and it turns out she is severely intolerant to sorbitol. So many things are sweetened with apple and pear juice, because they're cheap and sweet (like "kiwi-strawberry juice", where the first ingredient is apple juice, for example) And sorbitol is used as an artificial sweetener. It can affect different people different ways (constipation, very loose stools, it depends.
And by the way, green grapes are chemically different from red or purple, so 100% unsweetened white grape juice (which is fairly easy to find) is a good choice.
This is a pretty easy thing to try, so you might experiment. You'll have to really read labels, though!