Poor little thing - This is going to sound really stupid & I'm sure its been ruled out . The formula he is having , is it hypo allergenic? He hasnt got a intolerance to protein in cows milk?? May be worth bringing this up . My 4yr old had it picked up within the first 72hrs of being born , but they carried on ruling out any other possible reasons too.
It also annoyed me when my youngest was in NICU that they expected her to take 66mls of milk each feed, the first 45mls she would take, then the rest was hard work. That got put through the NG tube in the end. I queried why they expect the full 66mls each feed , as we don't eat the same amount each mealtimes ourselves. After a week of her still taking the same amount, they agreed that that was her capacity.
Hope you get to the root cause of whats going on though .