Startup Applications does not show all applications
From WickyWiki
Show all items in the folder /etc/xdg/autostart/ to be able to enable en disable then in the Startup Manager. You might need to repeat this after installing new appliciations.
sudo sed --in-place 's/NoDisplay=true/NoDisplay=false/g' /etc/xdg/autostart/*.desktop
Now you can configure what applications are started automatically when you startup.
gnome-session-properties
See also: