From Ubuntu Precise, most startup apps have been hidden from the Startup Applications window, so all user sees when he opens this via settings is a subset of applications at startup. To display all the startup apps, all you need to do is to open up terminal and type:

sudo sed -i 's/NoDisplay=true/NoDisplay=false/g' /etc/xdg/autostart/*.desktop

Provide your password if required. Now if you open Startup Applications from settings you will see all the applications at startup and disable them if required.

Disabling unneeded startup apps will significantly speed up bootup time.