I'll ditto Matt's post, less the website which I haven't seen, and add
I believe the root cause to be a variation in coefficient of friction
around the circumference the rotor. Pads leaving material in various
places on the rotor is one way to cause this variation in friction.
Another way for this to occur is simply via corrosion. If you leave
your car sit for a few days outside (or just overnight in some areas),
you'll see some light rust on the rotors (if you can see through the
wheels). Roll the vehicle so that each wheel makes about half a turn,
and you'll see that there's an absence of rust on the portion of the
rotor which was behind the pad. Over time, the rotor accrues varying
levels of corrosion around its circumference.
In most cases, I'm unable to make the problem go away by hard
braking. When resurfaced, rotors display little runout, but after
resurfacing, the problem is gone. This leans me toward the latter
issue rather than the former, since the corrosion does eat away
unevenly at the surface, even if it isn't noticeable with the eye.