Root motion deforms model on certain animations

I created a 3D character in 3D Studio Max 2014. This model was fully rigged, skinned and animated using bones and controllers. The animations were then baked into the bones and controllers and exported as FBX. When imported into Unity 5 the animations run well, selecting a root node causes some deformation which can be corrected on most animations messing with the root transforms. Activating "bake into pose" and setting based upon on "original" help for the most part, but there are 2 animations that just twitch and deform. These animations are a turning animation while idle and a stopping animation while running.

I've tried to export the model selecting only the mesh, IKs and bones but the controllers seem to still attach to the model. Baking the animation to the bones seem not to complete create all the needed frames. Maybe if there is a way to bake the animations to the bones making them independent from the controllers could solve part of the problem, but I'm not sure.

I've also though that maybe it's a hierarchy problem with the bones, but I've done the complete rig running through a tutorial on Digital Tutors. Problem is they just don't explain how to bake the animations for Unity.

Here is a comparison between a frame in 3DS and Unity from the turning animation.

As you can see the deformation seems to come from the hips or spine for some reason. Same happens for the stopping animation below.

Any suggestions are welcomed!