Menu won't hide when loading different scene

Okay, so I've been searching for about an hour now, and I can't find a solution at all. I started this project earlier today and it's my first project using Unity. I followed the very first tutorial on the site "Roll a Ball". I have then been using it as a baseline to expand it into something different (eventually). I've been playing around with little bits of code here and there, and adding little bits to get a grip for it all.

However now I am stuck. I have a menu page which allows me to start game, load game (which in itself gives a warning because that feature isn't implemented yet) and a quit game button.

It looks like this; http://i.gyazo.com/524684969a803a4a7c89a9e01a3ea45d.png

The problem I am having is this: http://i.gyazo.com/8d95ac9db707b40e38b2d85c2ecc400a.png

Here is the code below.

Menu.cs

 using UnityEngine;
 using System.Collections;
 using CorruptedSmileStudio.MessageBox;
 
 public class Menu : MonoBehaviour 
 {
     void OnGUI () 
     {
         // Make a background box
         GUI.Box (new Rect (10, 10, 100, 120), "Main Menu");
             
         // Make the first button. If it is pressed, Application.Loadlevel (1) will be executed
         if (GUI.Button (new Rect (20, 40, 80, 20), "Start Game")) 
         {
             Application.LoadLevel (1);
         }
 
         // second button
         if (GUI.Button (new Rect (20, 70, 80, 20), "Load Game")) 
         {
             MessageBox.Show (null, "I'm sorry, but the load game feature is not current avalible in this build.", "Load Game Feature", MessageBoxButtons.OK, MessageBoxIcon.Information);
         }
             
         // Make the third button.
         if (GUI.Button (new Rect (20, 100, 80, 20), "Quit")) 
         {
             Application.Quit ();
         }
     }
 }

PlayerController.cs

 using UnityEngine;
 using UnityEngine.UI;
 using System.Collections;
 
 public class PlayerController : MonoBehaviour 
 {
 
     public float speed;
     public Text winText;
 
     private Rigidbody rb;
     private int count;
     private float timer;
 
     void Start()
     {
         rb = GetComponent<Rigidbody> ();
         count = 0;
         timer = 0.0f;
     }
 
     void FixedUpdate()
     {
         if (count < 11) 
         {
             timer += Time.deltaTime;
         }
 
         float moveHorizontal = Input.GetAxis ("Horizontal");
         float moveVertical = Input.GetAxis ("Vertical");
 
         Vector3 movement = new Vector3 (moveHorizontal, 0.0f, moveVertical);
 
         rb.AddForce (movement * speed);
 
         CheckIfWon ();
     }
 
     void OnTriggerEnter(Collider other)
     {
         if (other.gameObject.CompareTag ("Pick Up")) 
         {
             other.gameObject.SetActive (false);
             count = count + 1;
         }
     }
 
     void CheckIfWon ()
     {
         if (count >= 11) 
         {
             Application.LoadLevel(0);
         } 
     }
 
     void OnGUI() 
     {
         GUI.Box(new Rect(5, 0, 100, 20), "Cubes: " + count.ToString("0")); // score
         GUI.Box(new Rect(5, 20, 100, 20), "Time: " + timer.ToString("0")); // timer
     }
 }

Thanks for any, and all helpful responses. :)