When including a system menu, any similar user entries (additional submenus, for example) are sorted below the entire system menu, whereas it'd be quite swell to have them sort among the system menu, so that the end result would be an alphabetised menu.
unfortunately, this isn't possible with the current system, and i don't think it's a good idea to automatically sort, as there's the potential to order items in the toplevel menu that's undesireable. i'll think about adding a sorted=(true|false) property for menus, however.
Not going to happen with the current menu system. If Jannis ends up writing a real freedesktop.org-compliant implementation for 4.6, this will Just Work[tm].