Highscoring and changing scripts (Java/UnityScript)

Well, update is called once a frame, if you're using Update and your addscore function, i would ditch the guiText.text change in addscore, such a waste of time as it will be picked up on the next frame Update function call.

  #pragma strict
  var Counter : int = 0;
  
  function addscore () {
    Counter += 1;
  }
  
  function Update () {
    Debug.Log("updated Guitext.text");
    guiText.text = "Score:" + Counter.ToString();
  }
  
  function endlevel (){
    var oldHighscore : int = PlayerPrefs.GetInt("Highscore", 0); // second parameter is for default value if not found in player prefs.
    
    if (Counter > oldHighscore) {
     PlayerPrefs.SetInt("Highscore", Counter); // if the current score(counter) is greater than the old $$anonymous$$ghscore, then you have beaten it.
     PlayerPrefs.Save(); // After setting, save/commit the new value(s).
    }
    
    guiText.text = "Score:0";
    Counter = 0;
  }

if you want to pull it in the other script:

 #pragma strict
  var High : int;
  
  function Start () {
    High = PlayerPrefs.GetInt("Highscore", 0); // again, second parameter is default if not found yet.
    guiText.text = "Highscore:" + High.ToString();
  }