It also depends on which bone (game object) you assign the hit spheres to. The default setup has the spheres follow the location of the bone during animation for automatic placement.
Also, the screens are misleading. The first one you're viewing from the Z axis and the right one you're viewing from the x axis.
So everything's correct since the game doesn't put the hit spheres anywhere on the z-axis except at point 0. When you get the character in game it will follow the bones you have assigned, in their animation, on the x and y axes exclusively. What you're seeing is your character going from a "facing background" position, and you're turning them to "face forward" position. I imagine you don't have any offsets on the bone links so you're seeing everything from the character's right side positioning.