I asked this question many years ago on a Usenet group, and the answer was along the lines of what we're seeing is many millions of years after those orbits began, and that they all eventually flatten out due to the gravity of the other objects in orbit.
So you could have 2 objects at roughly the same orbital distance but perpendicular to one another (eg. one orbiting the star's poles and the other around it's equator), and over time the small amount of gravitational force they exert on one another will bring them roughly into the same plane.
Hopefully someone better versed in the topic can come along to explain it better than I can.