Something seems wrong with the layout, JButton showing unexpected behaviour at resize of the window

The problem with your very nice example may be platform dependent, but I can offer a few observations:

• You’re not adding or removing components, so you don’t need revalidate().

• Because the background color is a bound property of the buttons, you don’t need the subsequent calls to repaint().

• You do need repaint() in your custom DrawingArea, but you may want to experiment with adding property change support, as suggested here.

• Color.white can’t be brighter() and Color.black can’t be darker(); Color.darkGray.darker() is Color.black().

• The variation below uses a Queue<Color> to simplify changing colors.

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.Queue;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
import javax.swing.Timer;

/** @see https://stackoverflow.com/q/9849950/230513 */
public class BallAnimation {

    private int x;
    private int y;
    private boolean positiveX;
    private boolean positiveY;
    private boolean isTimerRunning;
    private int speedValue;
    private int diameter;
    private DrawingArea drawingArea;
    private Timer timer;
    private Queue<Color> clut = new LinkedList<Color>(Arrays.asList(
        Color.BLUE.darker(),
        Color.MAGENTA.darker(),
        Color.BLACK,
        Color.RED.darker(),
        Color.PINK,
        Color.CYAN.darker(),
        Color.DARK_GRAY,
        Color.YELLOW.darker(),
        Color.GREEN.darker()));
    private Color backgroundColour;
    private Color foregroundColour;
    private ActionListener timerAction = new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent ae) {
            x = getX();
            y = getY();
            drawingArea.setXYColourValues(x, y, backgroundColour, foregroundColour);
        }
    };
    private JPanel buttonPanel;
    private JButton startStopButton;
    private JButton speedIncButton;
    private JButton speedDecButton;
    private JButton resetButton;
    private JButton colourButton;
    private JButton exitButton;
    private ComponentAdapter componentAdapter = new ComponentAdapter() {

        @Override
        public void componentResized(ComponentEvent ce) {
            timer.restart();
            startStopButton.setText("Stop");
            isTimerRunning = true;
        }
    };

    public BallAnimation() {
        x = y = 0;
        positiveX = positiveY = true;
        speedValue = 1;
        isTimerRunning = false;
        diameter = 50;
        backgroundColour = Color.white;
        foregroundColour = clut.peek();
        timer = new Timer(10, timerAction);
    }

    private void createAndDisplayGUI() {
        JFrame frame = new JFrame("Ball Animation");
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.setLocationByPlatform(true);

        drawingArea = new DrawingArea(x, y, backgroundColour, foregroundColour, diameter);
        drawingArea.addComponentListener(componentAdapter);

        frame.add(makeButtonPanel(), BorderLayout.LINE_END);
        frame.add(drawingArea, BorderLayout.CENTER);
        frame.pack();
        frame.setVisible(true);
    }

    private JPanel makeButtonPanel() {
        buttonPanel = new JPanel(new GridLayout(0, 1));
        buttonPanel.setBorder(BorderFactory.createLineBorder(Color.darkGray, 5));

        startStopButton = new JButton("Start");
        startStopButton.setOpaque(true);
        startStopButton.setForeground(Color.white);
        startStopButton.setBackground(Color.green.darker());
        startStopButton.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent ae) {
                if (!isTimerRunning) {
                    startStopButton.setText("Stop");
                    timer.start();
                    isTimerRunning = true;
                } else if (isTimerRunning) {
                    startStopButton.setText("Start");
                    timer.stop();
                    isTimerRunning = false;
                }
            }
        });
        startStopButton.setBorder(BorderFactory.createLineBorder(Color.gray, 4));
        buttonPanel.add(startStopButton);

        colourButton = new JButton("Change Color");
        colourButton.setOpaque(true);
        colourButton.setForeground(Color.white);
        colourButton.setBackground(clut.peek());
        colourButton.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent ae) {
                //timer.restart();
                clut.add(clut.remove());
                foregroundColour = clut.peek();
                drawingArea.setXYColourValues(x, y, backgroundColour, foregroundColour);
                colourButton.setBackground(foregroundColour);
            }
        });
        colourButton.setBorder(BorderFactory.createLineBorder(Color.gray, 4));
        buttonPanel.add(colourButton);

        exitButton = new JButton("Exit");
        exitButton.setBackground(Color.red);
        exitButton.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent ae) {
                timer.stop();
                System.exit(0);
            }
        });
        exitButton.setBorder(BorderFactory.createLineBorder(Color.red.darker(), 4));
        buttonPanel.add(exitButton);

        return buttonPanel;
    }

    private int getX() {
        if (x < 0) {
            positiveX = true;
        } else if (x >= drawingArea.getWidth() - diameter) {
            positiveX = false;
        }
        return (calculateX());
    }

    private int calculateX() {
        if (positiveX) {
            return (x += speedValue);
        } else {
            return (x -= speedValue);
        }
    }

    private int getY() {
        if (y < 0) {
            positiveY = true;
        } else if (y >= drawingArea.getHeight() - diameter) {
            positiveY = false;
        }
        return (calculateY());
    }

    private int calculateY() {
        if (positiveY) {
            return (y += speedValue);
        } else {
            return (y -= speedValue);
        }
    }

    public static void main(String... args) {
        Runnable runnable = new Runnable() {

            @Override
            public void run() {
                new BallAnimation().createAndDisplayGUI();
            }
        };
        SwingUtilities.invokeLater(runnable);
    }
}

class DrawingArea extends JComponent {

    private int x;
    private int y;
    private int ballDiameter;
    private Color backgroundColor;
    private Color foregroundColor;

    public DrawingArea(int x, int y, Color bColor, Color fColor, int dia) {
        this.x = x;
        this.y = y;
        ballDiameter = dia;
        backgroundColor = bColor;
        foregroundColor = fColor;
        setBorder(BorderFactory.createLineBorder(Color.DARK_GRAY, 5));
    }

    public void setXYColourValues(int x, int y, Color bColor, Color fColor) {
        this.x = x;
        this.y = y;
        backgroundColor = bColor;
        foregroundColor = fColor;
        repaint();
    }

    @Override
    public Dimension getPreferredSize() {
        return (new Dimension(500, 400));
    }

    @Override
    public void paintComponent(Graphics g) {
        g.setColor(backgroundColor);
        g.fillRect(0, 0, getWidth(), getHeight());
        g.setColor(foregroundColor);
        g.fillOval(x, y, ballDiameter, ballDiameter);
    }
}