Helium freezes into a solid form within the clouds of Saturn, removing it preferentially from the atmosphere.
A large comet probably impacted Saturn, heating it up and driving much of the helium into orbit.
Saturns greenhouse effect causes helium to be heated up and thus escape the gravitational field of the planet..
Helium dissolves in hydrogen at the temperatures and pressures thought to exist in Saturns interior..
Helium may have liquefied and precipitated down into the interior of Saturn, reducing its overall contribution to the atmospheric composition.