Is your baby taking enough formula? Check with your doctor, sometimes we forget that children grow up and they need more protein.
is it possible that he has an infection? Did you check for cystitis or otitis?
Is he taking enough calories? As he grows up he needs energy. If he doesn t get it he will break down his own protein and you will have increase in phe.
Could it be a food he is eating that you think is low pro but it is really higher?
At the end maybe he cannot handle all the protein he is having. Last summer, my daughter after a phe tolerance test ended up with 600 mg per day. But during winter she stopped growng up and furthermore little subclinical viruses led to higher levels. So we lowered the intake to 400 and her levels went back to normal. Now we increase the intake again and she tolerates it well.