Cannot get only 1 box to move. Java 1.7 + LWJGL 2.9.1 in NetBeans

I am going through several tutorials and managed to create a display with 2 rendered squares. The problem I have is that when I move one square, the other moves at the same time. I only want one of the squares to move. I did a search here and used Google, but could not locate an article on this specific issue. Below is the code I am using, any ideas? I know I have to add a timer (ticks) and more, but I am trying to get a prototype done.


package worldofadventure;

/**
 *
 * @author Stoofus
 */

// Start imports
import static org.lwjgl.opengl.GL11.*;
import static org.lwjgl.util.glu.GLU.*;
import java.io.IOException;
import java.util.logging.FileHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.lwjgl.LWJGLException;
import org.lwjgl.input.Keyboard;
import org.lwjgl.input.Mouse;
import org.lwjgl.opengl.Display;
import org.lwjgl.opengl.DisplayMode;

// End imports

// Start class Main
public class Main
{

    /**
     * @param args the command line arguments
     */
    
    // Start variables
    static String TITLE = "World of Adventure - PreAlpha version 0.0.1";
    static int S_WIDTH = 800; // Screen Width
    static int S_HEIGHT = 600; // Screen Height
    static final Logger LOGGER = Logger.getLogger( Main.class.getName() );
    int squareSize; // Size of the square
    int squareX; // Horizontal location of the square
    int squareY; // Vertical location of the square
    int squareZ; // Depth of the square relative to the viewer
    
    int rectSize; // Size of rectangle
    int rectX; // Horizontal location of rectangle
    int rectY; // Vertical location of rectangle
    int rectZ; // Depth of rectangle relative to the viewer
    // End variables
    
    // Add a log handler and create a log file
    static
    {
        try
        {
            LOGGER.addHandler( new FileHandler("errors.log", true));
        }
        catch( IOException ex )
        {
            LOGGER.log( Level.WARNING, ex.toString(), ex );
        }
    } // End log handler
    
    // Start main program
    public static void main(String[] args) 
    {
        // Start the main GUI
        mainGUI myGUI = new mainGUI(); // Create myGUI object
        myGUI.setTitle( TITLE ); // Set title
        myGUI.setVisible( true ); // Set visable to true
        
    } // End main program
    
    // Start class startGame
    public void startGame()
    {
        Main main = null; // Create a null object
        try
        {
            // Print out mapped keys
            System.out.println( "Keys:" );
            System.out.println( "Q = Shrink" );
            System.out.println( "E = Grow" );
            System.out.println( "W = Up" );
            System.out.println( "S = Down" );
            System.out.println( "A = Left" );
            System.out.println( "D = Right" );
            System.out.println( "Esc = Exit" );
            main = new Main(); // Create an instance of the object
            main.create(); // Create the display
            main.run(); // Run the display
        }
        // Ooops, record what went wrong
        catch( Exception ex )
        {
            LOGGER.log( Level.SEVERE, ex.toString(), ex );
        }
        finally
        {
            if (main != null )
            {
                main.destroy(); // Destroy the instance of the object
            }
        }
    } // End class startGame
    
    // Start Main constructor
    public Main()
    {
        // Initialize variables
        squareSize = 100; // Initial size of square
        squareX = 55; // Initial X (Horizontal) position of square
        squareY = 50; // Initial Y (Vertical) position of square
        squareZ = 0; // Initial Z position of square
        
        rectSize = 100; // Initial size of rectangle
        rectX = 200; // Initial X (Horizontal) position of rectangle
        rectY = 50; // Initial vertical position of rectangle
        rectZ = 0; // Initial Z position of rectangle
    } // End Main constructor
    
    // Start class create
    public void create() throws LWJGLException
    {
        // Display
        // S_WIDTH = Display Width
        // S_HEIGHT = Display Heigh
        Display.setDisplayMode( new DisplayMode( S_WIDTH, S_HEIGHT ) );
        Display.setFullscreen( false );
        Display.setTitle( TITLE ); // Same title of mainGUI
        Display.create(); // Create the display object
        
        // Create keyboard
        Keyboard.create();
        
        // Create and ungrab mouse
        Mouse.setGrabbed( false );
        Mouse.create();
        
        // Initialize OpenGL
        initGL();
        resizeGL();
    } // End class create
    
    // Start class destroy
    // This method already checks if they have been created
    // before destroying them
    public void destroy()
    {
        Mouse.destroy();
        Keyboard.destroy();
        Display.destroy();
    } // End class destroy
    
    // Start class initGL
    // Creates the background
    public void initGL()
    {
        // 2D Initialization
        glClearColor( 0.0f, 0.0f, 0.0f, 0.0f );
        glDisable( GL_DEPTH_TEST );
        glDisable( GL_LIGHTING );
        
    } // End class initGL
    
    // Start class processKeyboard
    public void processKeyboard()
    {
        // Square's X axis
        if( Keyboard.isKeyDown( Keyboard.KEY_W ) )
        {
            // Move square up
            ++squareY;
        }
        if ( Keyboard.isKeyDown( Keyboard.KEY_S ) )
        {
            // Move square down
            --squareY;
        }
        
        // Square's Z axis
        if ( Keyboard.isKeyDown( Keyboard.KEY_A ) )
        {
            // Move square left
            --squareX;
        }
        if ( Keyboard.isKeyDown( Keyboard.KEY_D ) )
        {
            // Move square right
            ++squareX;
        }
        
        // Shrink or Grow square
        if ( Keyboard.isKeyDown( Keyboard.KEY_Q ) )
        {
            // Shrink square
            --squareSize;
        }
        if ( Keyboard.isKeyDown( Keyboard.KEY_E ) )
        {
            // Grow square
            ++squareSize;
        }
    } // End class processKeyboard
    
    // Start class processMouse
    public void processMouse()
    {
        // Enter mouse code here
    } // End class processMouse
    
    // Start class render
    public void render()
    {
        glClear( GL_COLOR_BUFFER_BIT );
        glLoadIdentity();
        
        // Translate into view for square
        glTranslatef( squareX, squareY, 0.0f );
        glRotatef( squareZ, 0.0f, 0.0f, 1.0f );
        glTranslatef( -( squareSize >> 1 ), -( squareSize >> 1 ), 0.0f );
        glColor3f( 0.0f, 0.5f, 0.5f );
        
        // Square
        glBegin( GL_QUADS );
            glTexCoord2f( 0.0f, 0.0f ); glVertex2f( 0.0f, 0.0f );
            glTexCoord2f( 1.0f, 0.0f ); glVertex2f( squareSize, 0.0f );
            glTexCoord2f( 1.0f, 1.0f ); glVertex2f( squareSize, squareSize );
            glTexCoord2f( 0.0f, 1.0f ); glVertex2f( 0.0f, squareSize );
        glEnd();
        
        // Translate into view for rectangle
        glTranslatef( rectX, rectY, 0.0f );
        glRotatef( rectZ, 0.0f, 0.0f, 1.0f );
        glTranslatef( -( rectSize >> 1 ), -( rectSize >> 1 ), 0.0f );
        glColor3f( 0.0f, 0.5f, 0.5f );
        
        glBegin( GL_QUADS );
            glTexCoord2f( 0.0f, 0.0f ); glVertex2f( 0.0f, 0.0f );
            glTexCoord2f( 1.0f, 0.0f ); glVertex2f( rectSize, 0.0f );
            glTexCoord2f( 1.0f, 1.0f ); glVertex2f( rectSize, rectSize );
            glTexCoord2f( 0.0f, 1.0f ); glVertex2f( 0.0f, rectSize );
        glEnd();
        
    } // End class render
    
    // Start class resizeGL
    public void resizeGL()
    {
        // 2D Scene
        glViewport( 0,0, S_WIDTH, S_HEIGHT );
        glMatrixMode( GL_PROJECTION );
        glLoadIdentity();
        gluOrtho2D( 0.0f, S_WIDTH, 0.0f, S_HEIGHT );
        glPushMatrix();
        glMatrixMode( GL_MODELVIEW );
        glLoadIdentity();
        glPushMatrix();
    } // End class resizeGL
    
    // Start class run
    public void run()
    {
        while( !Display.isCloseRequested() &&
                !Keyboard.isKeyDown( Keyboard.KEY_ESCAPE ) )
        {
            if ( Display.isVisible() )
            {
                processKeyboard();
                processMouse();
                update();
                render();
            }
            else
            {
                if( Display.isDirty() )
                {
                    render();
                }
                try
                {
                    Thread.sleep( 100 );
                }
                catch( InterruptedException ex )
                {
                    
                }
            }
            Display.update();
            Display.sync( 60 );
        }
    } // End class run
    
    // Start class update
    public void update()
    {
        
        int squareEdge = (squareSize / 2 ); // Find the edge via its size
        int rectEdge = ( rectSize / 2 ); // Ditto
        
        // Don't go offscreen from bottom
        if ( squareY < 50 )
        {
            squareY = 50;
        }
        // Don't go offscreen from top
        if ( squareY > S_HEIGHT - squareEdge )
        {
            squareY = S_HEIGHT - squareEdge;
        }
        // Don't go offscreen from left
        if ( squareX < squareEdge)
        {
            squareX = squareEdge;
        }
        // Don't go offscreen from right
        if ( squareX > S_WIDTH - squareEdge )
        {
            squareX = S_WIDTH - squareEdge;
        }
        
        // Don't get too small to see
        if ( squareSize < 5 )
        {
            squareSize = 5;
        }
        // Don't get bigger than the screen
        if ( squareSize > S_HEIGHT )
        {
            squareSize = S_HEIGHT;
        }
    } // End class update
    
} // End class Main

Thanks to Troubleshoots for the code tag suggestion! I kept comments to assist with the troubleshooting.