Scene gameobject public variables assigned by script in editor doesnot persist - but manually entered values in editor UI persists

Hi Guys, Im facing problem with uniquely taging unity gameobjects. I want to assign unique tag to gameobjects that persists. But every time I run this method a new tag is assigned to gameobjects in scene. Is there something I need to do to fix this issue ?

If I execute this method (TagButtons : mentioned below) many times; tags are assigned and are shown fine in unity editor but tags older values are read in script. If I edit values in editor they are stored correctly in unity. But somehow values are not storing correctly when editing values through script.

  [MenuItem("PMS/Tag Buttons")]
  public static void TagButtons()
  {
        TagScenesGameObjects();
  }

  public static void TagScenesGameObjects()
  {
      string[] allScenes = GetAllScenes();
      foreach (string scene in allScenes)
      {
          EditorSceneManager.OpenScene(scene);
          GameObject[] sceneGOs = GetAllObjectsInScene();
          foreach (GameObject gameObject in sceneGOs)
          {
              Button[] btnList = gameObject.GetComponents<Button>();
              foreach (Button btn in btnList)
              {
                  ButtonController buttonController = btn.gameObject.GetComponent<ButtonController>();
                  // First time add a valid new tag
                  if (buttonController == null)
                  {
                      buttonController = btn.gameObject.AddComponent<ButtonController>();
                      buttonController.SetTags(tag);
                  }
                  else
                  {
                      string tag = buttonController.GetTags();
                      string validTag = ValidTag(tag);
                      buttonController.SetTags(validTag);
                      EditorUtility.SetDirty (btn.gameObject);
                  }
              } 
          }
      }
  }