Ninjitsu is the "original" free-running style you could say. The training nowadays just doesn't focus on those techniques as much.
Hmm, yeah, you could say that. Of course, you would be wrong, though.
Free-running and parkour are rather removed from the ideas, concepts, movement, and ideals on Ninjutsu in a number of ways, really, both modern practice and historical usage. The problem comes when people think of popular imagery as being historically based (running, jumping, leaping over things, etc). There are traditional running methods, but they are very removed. There are traditional methods of climbing walls, but they are very far removed. There are ways of scaling buildings both up and down, but they are very far removed.
In the early 80's, Steve Hayes held a Shadows of Iga Festival in the US (one of the first), and sponsored Hatsumi Sensei to come out for it (to teach and observe). There are a number of stories about that time, but the relevant one here is when Hayes had his students demonstrate a method of moving down a cliff/outside a wall, which Hayes had consulted the SWAT forces for how to exactly do it. Hatsumi watched, and told everyone that it was very well done.... then pulled Hayes aside, and explained that the method chosen was rather easy to spot for anyone from the ground, and would have resulted in a simple capture and probable death. Hayes was shattered... he had figured that as he had gotten it from the SWAT team, it must be effective and safe! The problem is, of course, that the SWAT team are part of the police force, and seen as the "good guys", so being spotted isn't such an issue (they're allowed to be there, they're acting in the public good). A Ninja, on the other hand, doesn't have that luxury if attempting to enter somewhere they shouldn't be....
Superficial similarities don't quite cut it, unfortunately. This is why whenever anyone tries to say that Spec Ops, SEALS, CIA etc are "modern Ninja", the responce is usually an immediate "NO THEY'RE NOT!"