With the fix for 6777277 there was introduced a minor side effect: if the user iconifies an untrusted Java window and then deiconifies it using the taskbar button, the window does not receive the input focus when running on Metacity window manager. Subsequent clicks on the taskbar do not give the focus either. The user has to click the Java window itself in order to give the focus.
Note: this issue is not reproducible on Compiz and KDE. It affects Gnome/Metacity only.