NPC gets up inside terrain (disconsidering the terrain collider)

In my game humanoid NPCs have a lot of physics interaction, specially when the player casts spells with explosions or turning of the enemy's gravity. All these interactions trigger a ragdoll in the game object (by a specific set of scripts that you can see here: http://answers.unity3d.com/questions/1164842/from-animation-to-ragdoll-and-back.html#comment-1238107).

When they fall back to the ground, one of these ragdoll system's scripts sends a Raycast to detect where they are to blend the actual position to start a getting up animation.

What is going wrong is that the moment they start to get up, their root changes to a y = 0, and the getting up animation occurs at this height (not on the top of the terrain mesh, or on the top of a building), and they stay there, only getting back to terrain level afterwards, because of the NavMeshAgent.

Here is the part of the code I'm using that resets the NPCs root position, so the animation occurs exactly where their body is (it can be very far away, as a consequence of an explosion, for example):

 //Now cast a ray from the computed position downwards and find the highest hit that does not belong to the character 
                 RaycastHit[] hits=Physics.RaycastAll(new Ray(newRootPosition,Vector3.down)); 
                 newRootPosition.y=0;
                 foreach(RaycastHit hit in hits)
                 {
                     if (!hit.transform.IsChildOf(transform))
                     {
                         newRootPosition.y=Mathf.Max(newRootPosition.y, hit.point.y);
                     }
                 }
 
                 transform.position=newRootPosition;

Any help would be appreciated...