The most plausible explanation is the http://en.wikipedia.org/wiki/Hygiene_hypothesis see also http://blogs.scientificamerican.com/disease-prone/2012/02/15...
> And how in the world would you know that?
How could it? If a vaccine could cause such a change so could any illness. A vaccine is just a piece of virus put where your body can notice it. Everything after that is entirely from the body.
For example rabies: Lethal right? But the body can actually clear the rabies virus with no trouble - almost. The trouble is that by the time the body gets rids of the virus it's too late.
So what do you do? You give the body the rabies virus ahead of time, and you do it in a way that prevents the person from actually getting sick. Then next time the body encounters rabies it's ready.
All vaccines work exactly this way: You let the person encounter the illness ahead of time. You make no change whatsoever in the person - all you are doing is making them slightly sick, but in a way that doesn't kill them.
Whatever change the vaccine causes, the illness also does - except the illness also causes damage as the virus replicates.