My buttons do not appear when paused?

Here try this dude:

 var paused : boolean = false;
 var pausedGUI : GUITexture;
 var gameName : String = "Game Paused";
 var skin:GUISkin;
 var pauseTexture : Texture2D;
 var windowRect0 : Rect = Rect (670, 250, 150, 50);
 var windowRect1 : Rect = Rect (670, 300, 120, 50);
 var windowRect2 : Rect = Rect (670, 350, 120, 50);
 var windowRect3 : Rect = Rect (670, 400, 120, 50);
 static var backgroundColor : Color;
  
 function Update () {
  
     if(Input.GetKeyDown("p") && paused == false){
      
         //IF GAME IS PAUSED
         Time.timeScale = 0;
         AudioListener.pause = true;
         Screen.showCursor = true;
         GUI.backgroundColor = Color.blue;
         guiTexture.texture = pauseTexture;
         //GUISkin.CreateInstance new.skin;
         paused = true;
      
     } 
 
     else if(Input.GetKeyDown("p") && paused == true) {
      
         //IF GAME IS NOT PAUSED
         AudioListener.pause = false;
         Time.timeScale = 1.0;
         Screen.showCursor = false;
         paused = false;
 
     }
 }
  
 
 function OnGUI () {
     //Make New Windows
     if(paused == true) {
         guiTexture.texture = pauseTexture;
         guiText.text = gameName;
         GUI.color = Color.green;        
         windowRect0 = GUI.Window (0, windowRect0, PauseWindow, "Resume Game");
         GUI.color = Color.yellow;        
         windowRect1 = GUI.Window (1, windowRect1, PauseWindow, "Load, Save Game");
         GUI.color = Color.yellow;        
         windowRect2 = GUI.Window (2, windowRect2, PauseWindow, "Load, Save Game");
         GUI.color = Color.yellow;        
         windowRect3 = GUI.Window (3, windowRect3, PauseWindow, "Load, Save Game");
     }
 }
 
 // Make the contents of the window.
 // The value of GUI.color is set to what it was when the window
 // was created in the code above.
 function PauseWindow (windowID : int) {
     if (GUI.Button (Rect (10,20,100,20), "Hello World"))
         print ("Got a click in window with color " + GUI.color);
 
     // Make the windows be draggable.
     GUI.DragWindow (Rect (0,0,10000,10000));
 }

Let me know what happens (I'm not hugely familiar with GUI windows my self, to be honest)

Well I know that this isn't exactly what you are trying to make but it should help you see if there is something wrong with your early script as this is the prototype pause I am using in a game I am currently developing. #pragma strict

 var pressed1 : boolean = false;
 var pressed2 : boolean = false;
 public static var paused : boolean = false;
 var sX : int;
 var sY : int;
 
 function Start(){
     sX = Screen.currentResolution.width;
     sY = Screen.currentResolution.height;
 }
 
 function Update () {
 if(Interaction.talking == false){
 if(Input.GetKeyDown(KeyCode.Escape) && pressed1 == false && pressed2 == false){
 pressed1 = true;
 paused = true;
 }
 
 if(pressed2 == true && pressed1 == true){
 pressed1 = false;
 pressed2 = false;
 paused = false;
 }
 }
 }
 
 function OnGUI(){
 
 if(pressed1 == true){
     if(GUI.Button(Rect(sX - (sX / 2 + 50),sY - (sY / 2 + 50),100,50), "Continue")){
         pressed2 = true;
     }
     if(GUI.Button(Rect(sX - (sX / 2 + 50),sY - (sY / 2 - 10),100,50), "Quit Game")){
         Application.Quit();
     }
 }
 
 }

Please note that this script is also using the size of the screen for positioning so you can probably ignore all the sX's and sY's XD.

Hello, i don't know what are you exactly trying to do, but i have a similar code in one game that pauses the game and shows a little menu to exit or restar the level, check it out, hope it helps.

 //On the Update() function            
 
 if (Input.GetKeyDown(KeyCode.Escape) && !isGamePaused)
             {
                 Time.timeScale = 0;
                 isGamePaused = true;
             }
             else if (Input.GetKeyDown(KeyCode.Escape) && isGamePaused)
             {
                 Time.timeScale = 1;
                 isGamePaused = false;
                 askToRestart = false;
             }
 
 //On the OnGUI() function 
  private void OnGUI()
     {
         if (isGamePaused && gameStarted)
         {
             if (!askToRestart)
             {
                 GUI.Box(new Rect(0, 0, Screen.width, Screen.height), "Pausa");
                 if (GUI.Button(new Rect(Screen.width / 2 - 100, Screen.height / 2 - 10, 90, 20), "Restart"))
                 {
                     askToRestart = true;
                 }
                 if (GUI.Button(new Rect(Screen.width / 2 , Screen.height / 2 - 10, 90, 20), "Exit"))
                 {
                     Application.Quit();
                 }
             }
             if (askToRestart)
             {
                 GUI.Box(new Rect(Screen.width / 2 - 100, Screen.height / 2 - 50, 200, 30), "¿Want to restart?");
                 if (GUI.Button(new Rect(Screen.width / 2 + 5, Screen.height / 2 - 10, 60, 20), "Si"))
                 {                    
                     Application.LoadLevel("GamePlayScene");
                 }
                 if (GUI.Button(new Rect(Screen.width / 2 -65, Screen.height / 2 - 10, 60, 20), "No"))
                 {
                     askToRestart = false;
                 }
             }
         }
 }