Mecanim system - character starts to float

I'm setting up a character with the mecanim system, and writing my own contoller at the same time. the problem I'm having is that with my run and running jump animations, the character starts to move up along the y axis and doesn't come back down completely - if I run and run-and-jump for a while eventually the character is floating in space.

I've fixed this by baking the y translation into the pose on both animations, but that seems to affect how the capsule collider follows the animation, although for the moment I've taken collider off so I only have the Animator and my script on the character as components right now.

Is this any kind of known issue, or is there something I've done incorrectly?