gajim is using Menu.popup() when right clicking the tray icon,
but should use popup_at(), as the menu could appear anywhere on
the screen otherwise. Yesterday, for example, it was basically
at the bottom left of the screen while the tray icon is in the
upper right.
log of #gnome-shell:
<halfline> gajim is doing: <halfline>
self.systray_context_menu.popup(None, None, None, event_button,
<halfline> event_time)
<halfline> the docs for that function say
<halfline> Note that this function does not work very well on GDK
backends that do not have global coordinates, such as Wayland or Mir.
You should probably use one of the gtk_menu_popup_at_ variants, which do
not have this problem