I just Googled "itchy cradle cap" and the Royal Children's Hospital (Melbourne) website says:

If it (the cradle cap) is continuing after your baby is three months old and/or it is very itchy for your baby, it may actually be eczema of the scalp. If this is the case, shampoos and salicylic acid creams will make it worse.
It may be worth taking him to a GP just to make sure it's not eczema?