I don't think it has to do with your milk? I'm pretty sure the 'milk' spots term is a bit outdated and not really accurate these days...
Natty had spots for about 6-8 weeks. I remember thinking when she was about 3 months old, 'oh wow, her skin's lovely!' LOL, I hadn't noticed the spots gradually disappearing. I think you just need to wait it out, unless it is bothering him (as a PP has already said).
Also, I second Christy's comments re J&J products: if you find your bub has sensitive skin, the fragrances in these products tend to make things worse.