Brian, microwaves alter the molecular structure of the sugars in milk so that an infant's gut enzymes can't completely digest them. You never want to heat the formula or milk so much that it changes colour indicating the sugars have cooked. That's why using your Anova is so useful, its precise control.
Maybe you have noticed that microwaves similarly alter starches making them tougher.
If your son tolerates heating your his milk on the stove i suggest you ask your Paediatrician about it. If he's older than a few months perhaps he has adapted to the modified sugars and is able to digest them and he has lost his natural digestive enzymes. If he had a course of antibiotics that could be a cause.
Infants are born with the necessary enzymes to digest human milk. Human milk changes over time introducing new digestive enzymes to your child. That's one of the reasons it's superior to formula.