Hi, my son has similar poopoo problem but instead of taking japanese formular milk, I took my doctor's advice to change a special formular milk for my son. It works, his poopoo is getting much much better. At the very beginning, I also doubt if it is necessary to change.
Why not u can ask yr doctor for second opinion? Like my doctor, she explained to me that many famous formular milk are too rich for baby, i.e. baby cannot absorb all nutrition and some babies are then having poopoo problem or some may not grow up that well even though they take quite a lot of milk.
My doctor is quite good and a very reasonable guy. She wrote a number of books too.