"Soke" simply means "main family," and can be used in a wide range of contexts, including arts other than the bugei. In bugei usage, "soke" refers to the founder's house, or to the current heir to the ryuha's formal headship; "shihanke" refers to the designated head instructor, or to a lineage of such instructors. A few traditions, like Kashima-Shinryu, claim dual/parallel lineages stretching way way back; in others shihanke are named in some generations and not in others. Usually (but not always), a shihanke is designated because the titular head of the school is for one reason or another unable to serve as the principal instructor.
Because "soke" refers to the family lineage, as well as the current headmaster, it's possible for some of the names on the list of "soke" to predate the actual ryuha. It's really just a matter of emphasis and choice on the part of the school--emphasizing the family tradition vs. emphasis on a particularly famous "founder".
It's best not to get too hung up on terms of this sort, because (like a good bit of Japanese vocabulary) their usage isn't always consistent and their meanings can be fairly amorphous.
It's also best not to take things like the beginnings of particular ryuha too seriously, since any dates or individuals cited are ultimately fairly arbitrary. The designation of any individual as the founder of a system is really only partly a matter of invention and innovation on the part of the "founder"; it's also a matter of politics and hagiography.
Bugei training and bugei ryuha did not become heavily formalized until the Tokugawa period. Before that, training for most warriors was an ad hoc mixture of learning from dad and your buddies, picking up on experience and inspiration of your own, plus scattered episodes of more structured coaching, sometimes from famous teachers (kind of like the way kids today learn to play basketball).
Obviously the "founders" of the various ryuha learned from someone somewhere, and the people who taught *them* must have learned somewhere too. If you want to, you could therefore trace any "school" back as far as you want, which is exactly what some ryuha do, when they speak of origins in the Heian period and such. When historians assert that ryuha bugei began around the 15th century, they mean that that was the point at which enough of the conventions, practices and traditions we now associate with the phenomenon began to appear to justify identifying the start of something new. Obviously, though, at least *some* of the information that defined the "new" ryuha had to have been around before this period--in fact you can follow that regression all the way back to the cavemen.
Karl Friday
Dept. of History
University of Georgia
Athens, GA 30602