so dont use windows l&f

so dont do it then

so dont use the windows L&F

so dont use it.

The JCB is actually 'above' the JL, here.

I did not see the stated problem, either way, but
noticed the very fragile code being used.

Use layouts.  This might not be exactly what you
want, it might require a nested layout to get the
full effect, but it is perhaps a starting point..

<sscce>
import java.awt.*;
import javax.swing.*;
import javax.swing.border.*;
import javax.swing.UnsupportedLookAndFeelException;

public class AltKeyRepaint {
   public static void main(String args[]) throws ClassNotFoundException,
           InstantiationException, IllegalAccessException,
           UnsupportedLookAndFeelException {
       // Use the System (i.e. "Windows") L&F
       // ie only if the user is Window'd
       // otherwise it will be the Mac. or *nix style PLAF's
       javax.swing.UIManager.setLookAndFeel(javax.swing.UIManager
               .getSystemLookAndFeelClassName());

       // The frame to display the sample
       JFrame frame = new JFrame("Frame");
       frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

       // this is probably not only the source of the
       // current problems, but a dozen others that
       // have either not been seen, or not manifested yet.
       // Do not use 'null' layouts unless you..
       //  a) know what your doing, (and potentially also..)
       //  b) are designing a custom layout,
       // frame.getContentPane().setLayout(null);
       JPanel p = new JPanel(new BorderLayout());
       p.setBackground(Color.ORANGE);

       // A big colored label in the background
       JLabel label = new JLabel("A sample label in the CENTER",
           JLabel.CENTER);
       label.setOpaque(false);
       // play with the padding numbers,
       // to get the right effect..
       label.setBorder( new EmptyBorder(30,15,50,15) );

       // A check box on top of the background label
       JCheckBox chkBox = new JCheckBox("a check box in NORTH");
       chkBox.setOpaque(false);
       chkBox.setBorder( new EmptyBorder(20,5,20,5) );

       // Add the label and check box to the frame
       p.add(chkBox, BorderLayout.NORTH);
       p.add(label, BorderLayout.CENTER);

       frame.getContentPane().add(p);

       // display it
       // deprecated in Java 1.2/1.5
       // frame.show();

       // this cause everything to become the
       // preferred size, which might be different
       // on different platforms, PLAF's, font sizes,
       // Java versions, or screen resolutions.
       frame.pack();
       frame.setLocationRelativeTo(null);
       frame.setVisible(true);
   }
}
</sscce>

HTH