The only thing that looks suspicious is in your .xsession-errors is:
(polkit-gnome-authentication-agent-1:2267): Gtk-CRITICAL **:
gtk_widget_destroy: assertion `GTK_IS_WIDGET (widget)' failed
** Also affects: aptdaemon (Ubuntu)
Importance: Undecided
Status: New
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Update manager hangs after authenticating, after a while reports "it seems that
the daemon died"
https://bugs.launchpad.net/bugs/445893
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