during investigation of 6458497 I have found that we have similar problems (in term of focus transfer) under X. Here is a simple test to reproduce the problem.
You need to press "press me" button and transfer focus out of the java.

import java.awt.AWTEvent;
import java.awt.FlowLayout;
import java.awt.Toolkit;
import java.awt.event.AWTEventListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.WindowConstants;

/**
 *
 * @author son
 */
public class bug6458497 {
    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        JFrame jframe = new JFrame("test for 6458497") {
            public String toString() {
                return "frame1";
            }
        };
        jframe.setLayout(new FlowLayout());
        JButton jbtn1 = new JButton("press me") {
            public String toString() {
                return "button1";
            }
        };
        jframe.add(jbtn1);
        final JButton jbtn2 = new JButton("I'm going to have a focus") {
            public String toString() {
                return "button2";
            }
        };
        jframe.add(jbtn2);
        jframe.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
        jframe.pack();

        jbtn1.addActionListener(new ActionListener() {
            public void actionPerformed(ActionEvent ae) {
                System.err.println("Got action, waiting...");
                try {
                    Thread.sleep(3000);
                } catch (InterruptedException ex) {
                    ex.printStackTrace();
                }
                System.err.println("requesting focus on jbtn2... " + jbtn2.requestFocus(false));
            }
        });
        jframe.setVisible(true);
        JFrame jframe2 = new JFrame("an opposite frame") {
            public String toString() {
                return "frame2";
            }
        };
        jframe2.add(new JButton("jbutton") {
            public String toString() {
                return "button3";
            }
        });
        jframe2.pack();
        jframe2.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
        jframe2.setVisible(true);
    }
}