Character controller Jumps while using Locomotion

Hi im a noob when I've been learning how to use locomotion via the downloadable step by step tut.

The problem I experience after setting up my character to be able to do a walk cycle when being dragged by the gizmos is that the "character controller" on my character jumps up and down when my character moves in any direction.

Since it does this the character passes right through other gameobjects (with colliders on) and doesn't step on them??

I have also moved the character with the character controller on to a different layer so as not to be raycasted by the locomotion system. Still doesn't make a difference??