GUI Layout flickering while exiting application

When user press back button for exit, I am showing a dialog made of GUI components. When i press yes button for exit the layout flickers for sometime and then the application exit. Here is the script .

 public class MainScreenGUIScript : MonoBehaviour 
 {
     public bool visible;
     public GUISkin customSkin;
 
     float screenWidth;
     float screenHeight;
 
      float dialogStartX;
      float dialogStartY;
      float dialogWidth;
      float dialogHeight;
 
      float DialoglabelX;
      float DialoglabelY;
 
      float DialogTitlelabelX;
      float DialogTitlelabelY;
 
      float DialoglabelWidth;
      float DialoglabelHeight;
 
      float DialogYesButtonX;
      float DialogYesButtonY;
 
      float DialogNoButtonX;
      float DialogNoButtonY;
 
      float DialogButtonWidth;
      float DialogButtonHeight;
 
     public GUIStyle boxBackgroundStyle;
     public GUIStyle yesButtonStyle;
     public GUIStyle noButtonStyle;
     public GUIStyle titleLabelStyle;
     public GUIStyle fbStyle;
     public GUIStyle settingStyle;
 
     float buttonWidth;
      float buttonHeight;
      float buttonY;
      float othersX;
      float backX;
 
     void Start () 
     {
         visible=false;
     }
     
     // Update is called once per frame
     void OnGUI()
     {
         GUI.skin = customSkin;
 
         screenWidth=Screen.width;
         screenHeight=Screen.height;
 
         dialogStartX=(float) (screenWidth*0.275);
         dialogStartY=(float) (screenHeight*0.35);
 
         dialogWidth=(float) (screenWidth*0.5);
         dialogHeight=(float) (screenHeight*0.28);
 
         DialoglabelWidth=(float) (screenWidth*0.3);
         DialoglabelHeight=(float) (screenHeight*0.1);
 
         DialoglabelX=(float) (screenWidth*0.415);
         DialoglabelY=(float) (screenHeight*0.45);
 
         DialogTitlelabelX=(float) (screenWidth*0.4);
         DialogTitlelabelY=(float) (screenHeight*0.36);
 
         DialogYesButtonX=(float) (screenWidth*0.36);
         DialogYesButtonY=(float) (screenHeight*0.54);
 
         DialogNoButtonX=(float) (screenWidth*0.55);
         DialogNoButtonY=(float) (screenHeight*0.54);
 
         DialogButtonWidth=(float) (screenWidth*0.15);
         DialogButtonHeight=(float) (screenHeight*0.08);
 
         buttonWidth=(float) (screenWidth*0.06);
         buttonHeight=(float) (screenHeight*0.08);
 
         othersX=(float) (screenWidth*0.9);
         backX=(float) (screenWidth*0.01);
         buttonY=(float) (screenHeight*0.89);
 
         if(GUI.Button(new Rect(othersX,buttonY,buttonWidth,buttonHeight),"",fbStyle))
         {
             if(!visible)
             {
                 Application.OpenURL ("");
             }    
         }
         if(GUI.Button(new Rect(backX,buttonY,buttonWidth,buttonHeight),"",settingStyle))
         {
             if(!visible)
             {
                 Application.LoadLevel(3);    
             }    
         }
         if(visible)
         {
             GUI.Box(new Rect(0,0,Screen.width,Screen.height),"");
             GUI.Box(new Rect(dialogStartX,dialogStartY,dialogWidth,dialogHeight),"",boxBackgroundStyle);
             GUI.Label(new Rect(DialogTitlelabelX,DialogTitlelabelY,DialoglabelWidth,DialoglabelHeight),"Quit",titleLabelStyle);
             GUI.Label(new Rect(DialoglabelX,DialoglabelY,DialoglabelWidth,DialoglabelHeight),"Do You Want To Quit ?");
             if(GUI.Button(new Rect(DialogYesButtonX,DialogYesButtonY,DialogButtonWidth,DialogButtonHeight),"",yesButtonStyle))
             {                
                 visible=false;
                 applicationExit();
             }
             if(GUI.Button(new Rect(DialogNoButtonX,DialogNoButtonY,DialogButtonWidth,DialogButtonHeight),"",noButtonStyle))
             {
                 visible=false;
             }
         }
         if (Input.GetKey(KeyCode.Escape))
            {
             visible=true;
         }    
     }
 
     void applicationExit()
     {
         Application.Quit();
     }
 }

Initially there are two GUI.Button which are visible. When user press back key(Android) I change the value of visible to true so that dialog appears . When user clicks on Yes Button I set value of visible to false and then call Application.Quit() it flickers and then application exit. What could be the reason.