This is just another technicality. AF-S is supposed to designate not only that the lens has internal focusing, but that it is also instantly over-rideable by turning the focus ring. However, Nikon neglected that capability in just a couple of lenses (it is probably cheaper to have a design that doesn't have an instant clutch mechanism to allow it to be over-ridden). So it appears the Nikon re-thought the "AF-S" designation for some of their kit lenses, in order to keep the internal focus motor. They probably knew that they were going to have future bodies without motors when they designed these lenses.
For some reason I don't understand why Nikon would put an AF-S on the 18-55 if it really wasn't an AF-S, like achuang says.