looking in to this further reveals that guake, as was mentioned, depends
on the notification system (when display notification on startup is
active) but the notification system is not launched at any well-defined
time, thus allowing guake to start sometimes prior to the notification
system sometimes after. Thus when guake starts before the notification
system, it crashes, when it starts after it displays the notification
and runs.

Therefore the problem as it pertains to this bug is that autostarted
applications aren't launched at a well-defined time making it impossible
to make assumptions about dependencies. Either well-defined hooks should
be made available or a priority list/order of startup applications
should be made or developers should be informed that as of gnome 3.4+
they can no longer make reliable assumptions about the order in which
applications are started at login.

As for the problem with guake, the easy work around is to simply disable
said notification in the guake preferences.

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https://bugs.launchpad.net/bugs/997112

Title:
  ~/.config/autostart doesn't work on gnome-shell

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