What is wrong with my code?

I have a lot of cubes and I select them with this script:

 #pragma strict
 function Update()
 {
     var ray = Camera.main.ScreenPointToRay (Input.mousePosition);
     var hit : RaycastHit;
  
     if(Input.GetMouseButtonDown(0))
     {
         if(Physics.Raycast(ray,hit,1000))
        { 
            if (hit.transform.tag == "cube")
            {
              hit.transform.tag="Untagged";
              hit.transform.renderer.material.color=Color.red;
              var cubes: GameObject[];
              cubes = GameObject.FindGameObjectsWithTag ("cube");
              for (var cube : GameObject in cubes) 
           {
                  cube.renderer.material.color=Color.black;
           }
           hit.transform.tag="cube";
                  Debug.Log("Cube is "+hit.transform.name);
  
                  
 }
 }
 }
 }

The problem is only right half of them are being selected. Here is a screenshot I took. Sorry for bad explanatation.

Thanks in advanced.