GUI Box not showing up after object clicked

Hello all. I am working on a project that requires the use to select a couple of objects, then once those objects are selected a test question shows up. The question then asks the user to select one of the objects to be able to continue.

All of that works right now, but the problem occurs when the object is clicked. I want a GUI Box to appear letting the user know if he clicked on the right object or not. After that a set of navigation buttons become available and the user can continue. The code is am using is:

if(allObjectsClicked  && isClicked ==false)
        {
            GUI.Box (new Rect (350,10,350,120), "Please RIGHT click the learning cube.");
            {
                if (Input.GetMouseButtonDown(1))
                {   
                    if (Physics.Raycast (ray, out hit))
                    {
                        if(hit.collider.gameObject.name == "learningCube2")
                        {
                            isClicked = true;
                            if(isClicked)
                            {
                                GUI.Box(new Rect (350,10,350,120), "Correct, you may now advance.");
                                navButtonEnabled = true;
                                Debug.Log("Why aren't you making the GUI box?");
                            }
                        }

                        else
                        {
                            isClicked = true;
                            if(isClicked)
                            {
                                GUI.Box(new Rect (350, 10, 350, 120), "Sorry, the correct answer was the cube. Click to advance.");
                                Debug.Log("Why are you still not making the GUI box?");
                                navButtonEnabled = true;
                            }//end isClicked
                        }//end else
                    }//end raycast hit
                }//end getmousebuttondown
            }//end GUI box
        }//end allObjectsClicked
    }//end popUpDisplayed
}//end testQuestionThree /**/

The problem is that the "Correct" or "Sorry" boxes aren't showing up, but it is printing to the debug log and the nav buttons are becoming available again. Everything runs without errors, just those two boxes won't show up.

That's because you've set conditions under which your box will appear. When you click the isClicked boolean will be true and does not match your "if" condition anymore, which requires to have the isClicked false in order to run through the block.