Running the test api/java_awt/Window/index.html#Ctor test Window2003 I noticed that it sometimes fails witn Motif toolkit enabled. This is against JDK6u12. Haven't tried other releases.

Standalone test (see below) is also failing with Motif if comment every System.* call out. Seem invocation of System*println() affects the time marked for pack() execution or something in native peers. Unfortunately, introducing the output in this test eliminates the failure in my environment.
This looks like a thread race and possibly may affect XAWT as well though I haven't seen that with XAWT for a long run.
Most likely that window size and pref.size are different.

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import java.awt.*;
import java.awt.event.*;

public class Window2003 {
    public static void main(String s[]) {
        Window win = null;
        try {
            Frame frame = new Frame("Title");
            win = new Window(frame);
            win.pack();

            System.out.println("size = "+ win.getSize());
            System.err.println("pref size = "+ win.getPreferredSize());

            // System.err.println("win is displayable = "+ win.isDisplayable());
            // System.err.println("frame is displayable = "+ frame.isDisplayable());

            // System.err.println("win is valid = "+ win.isValid());

            if(win.getSize().equals(win.getPreferredSize()) &&
                    win.isDisplayable() && frame.isDisplayable() &&
                    win.isValid()) {
                System.err.println("OKAY");
                return;
            }
            System.err.println("NOT OKAY ");
        } finally {
            win.dispose();
        }
    }
}
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