New research is suggesting that solar systems may be inherently unstable. You may have read recently that wandering inter-stellar planets may be more common than stars. The prediction is that planets frequently become ejected from their solar systems early in their formations, and wind up wandering deep space forever.
There is a complicated interaction within (and in some cases outside of) a solar system, will all the planets tugging on each other, affecting each other's orbits in subtle ways--and nearby stars may also influence the stability of a solar system. Since ejected planets seem to be so common, it would stand to reason that these planets are crossing each other's orbits at high speeds--migrating inwards toward the parent star, and throwing others out of the solar system.
It's my understanding that planets migrating inwards is the reason for the large number of hot jupiters and wandering planets.