To reproduce, configure the 'Window Buttons' plugin to always group windows. Now start a single instance of xeyes, minimize it and run the following command: 'wmctrl -r "xeyes" -b add,demands_attention'. Note that the minimized icon flashes. Close this instance of xeyes.

Now start two fresh instances of xeyes, minimize them and run the same wmctrl command, note that the grouped icon does not flash.