Character controller and mesh offset from each other, attempted corrections causing 'jump' to slow down?

Attempting to apply the examples of third person view character movement and animation from the textbook Unity in Action to a different model built in blender. When the model is placed in unity and given a character controller, the character controller is offset from the mesh. Moving the center of the character controller fixes this but causes the character to slow down and drift downwards after a 'jump'. Moving the 'metarig' corrects this, but the character again becomes offset from the character controller once animations are applied. Again after this, moving the center of the character controller causes the jump to slow down. I suspect this is an issue from the modelling, not unity itself, but can find nothing to support this hypothesis. What could be causing this behavior?