Indeed, reverting it fixes the bug for master. Again looks like you are better at diagnostics than me :)
I suppose we can just revert, since the reason why I moved the spinner out of the menu does not exists any more (no custom menu key-navigation any more, default menu nav. works fine with spinner inside menu)
Minor problem: I dont get the spinner adjusted to the right by using gtk_widget_set_hexpand (item, TRUE); + gtk_widget_set_halign (item, GTK_ALIGN_END) over the deprecated gtk_menu_item_set_right_justified. Any idea would be welcome !
All at all, I am surprised to see that such a flickering can happen, just because of the spinner location :F