The bug is described in the forums here http://forums.netbeans.org/post-98744.html but I could not find it in bugzilla.

The mouse cursor does not change to a resize cursor when hovering over window borders etc. after showing a modal progress dialog with ProgressUtils.showProgressDialogAndRun().

This happens because the main window glass pane is temporarily replaced by a translucent grey glass pane and when re-assigning the old glass pane it is changed to visible (although transparent) even though it was not before. This is because when calling JFrame.setGlassPane() the visibility of the new glass pane is set to the visibility of the previous glass pane.

It can be fixed by adding the following line in org.netbeans.modules.progress.ui.AbstractWindowRunner:

    private void ungrayMainWindow() {
        if (oldGlassPane != null) {
            JFrame jf = (JFrame) WindowManager.getDefault().getMainWindow();
            jf.setGlassPane(oldGlassPane);
            jf.getGlassPane().setVisible(false); // LINE ADDED FOR FIX!
            jf.invalidate();
            jf.repaint();
        }
    }