OK this is perfectly natural and nothing at all to worry about. Male dogs have two glands at the base of their penis which swell when they get excited. They are called the "Bulbus Glandis".
They have a purpose. During mating, they swell and keep the male dog inside the female more securely (when dogs mate they form a 'tie' when they get kind of stuck together for a while) This is nature's way to ensure the female will get pregnant.
Anyway, you may still notice them even after he has been neutered.
But don't worry. It's all ok.
ok so i just noticed the lumps are back, and i noticed it when he got a red rocket... please anyone HELP