This sounds extremely like my DS3, who was put on Nutramigen at 12mo when I stopped bf.
For a whole YEAR, I kept telling the GP I thought he was still allergic to the Nutramigen, and kept getting told no, no.
Finally his next dietician appointment came round. She was concerned because he had not grown OR put on even a pound in a whole year (as I kept telling the GP!!). Once I had described his symptoms, she got quite angry, told me that yes, he WAS still allergic to Nutramigen, and swapped him onto Neocate Active.
She fired off a snotty fax to the GP surgery too!!
He is like a totally different child now he is on Neocate. Proper poos, shooting up, filling out instead of looking scrawny, happier, not as grumpy, it's been amazing!
How the dietician explained it to me is : Nutramigen is protein based. The protein chains are broken down, but in a VERY allergic DC, the body will still recognise these broken down protein chains and react to them.
Neocate is based on Amino acids, and therefore the body has no protein chains to react to.
HTH.