This is reproducible with 6u12 b02 PIT build on Solaris. I show a Frame and click on the gnome-panel icon of the Frame. This minimizes the Frame first time. When I click on the icon of the Frame again, Frame gets restored. If the icon is clicked again, Frame stays instead of getting iconified. I've to click the icon 3-5 times to minimize the frame again.

To reproduce, run the below test, click on the gnome-panel icon of the frame. 
import java.awt.*;
public class TestFrame {
    public static void main(String[] args) {
        Frame f = new Frame();
        f.setSize(200, 200);
        f.setLocation(40, 40);
        f.setVisible(true);
    }
}