==UPDATE==
As per comments, here's a detailed description of my scene:
1 camera, 1 terrain (with a bunch of brushed in deformations), 1 directional light. I also have a .blend file in my Assets folder, which is automatically imported and I get my aStarCellHighlight prefab which is a cube with a transparency/diffuse texture:

to the camera I have attached to following script, to which I've then "bound" the terrain and aStarCellHighlight in the corresponding public fields:
public class RTSCamera : MonoBehaviour {
public Collider terrain;
public GameObject aStarCellHighlightPrefab;
private bool isCursorOnTerrain;
private RaycastHit cursorPositionOnTerrain;
private GameObject aStarCellHighlight;
void Start () {
cursorPositionOnTerrain = new RaycastHit();
aStarCellHighlight = (GameObject)Instantiate(aStarCellHighlightPrefab, terrain.transform.position, terrain.transform.rotation);
aStarCellHighlight.name = "cellHighlight";
aStarCellHighlight.transform.parent = terrain.transform;
}
void Update () {
trackCursorOnTerrain(false);
placeCellHighLight();
}
private void trackCursorOnTerrain(bool debug) {
Ray ray = this.camera.ScreenPointToRay(Input.mousePosition);
isCursorOnTerrain = terrain.Raycast(ray,out cursorPositionOnTerrain, 5000);
if(debug) {
if(isCursorOnTerrain) {
Debug.DrawLine (ray.origin, cursorPositionOnTerrain.point);
Debug.Log("terrainRight="+cursorPositionOnTerrain.point.x+" terrainUp="+cursorPositionOnTerrain.point.z+" terrainAltitude="+cursorPositionOnTerrain.point.y);
} else {
Debug.DrawLine (ray.origin, ray.GetPoint(5000));
}
}
}
private void placeCellHighLight() {
aStarCellHighlight.transform.localScale = new Vector3(50,50,200);
if(isCursorOnTerrain) {
aStarCellHighlight.transform.localPosition = cursorPositionOnTerrain.point + new Vector3(0,200,0);
} else {
aStarCellHighlight.transform.localPosition = Vector3.zero + new Vector3(0,200,0);
}
}
}
The script is supposed to basically draw a ray from camera's mouse cursor screen position to terrain, and then instantiate the Blender cube prefab, add is at a child of terrain, scale it to a visible size, and move it around on the terrain to where the mouse is, you know , "projecting" or whatever it is called.
when I hit play I the Blender prefab instance is created right away, it is shown as a descendat of terrain, is just not scaled properlly. Also if I move the mouse right away, the cube doesn't move with it:

Finally, if I just wait 10-20 seconds, the cube gets scaled, and now it moves with the cursor on the terrain:

Thanks for all any help!