I am using Arch Linux, and in Enlightenment 0.20.7, none of my "Startup Applications" are running when I start Enlightenment. This problem seems to only occur when Enlightenment is started via LXDM, thus running under X. If I run enlightenment_start from a text console - which launches Enlightenment via Wayland - then my startup applications are ran.
This issue did not occur in version 0.20.6, so I have downgraded back to that version.
The startup applications are .desktop files stored in /etc/xdg/autostart. In Enlightenment's settings, under Apps > Startup Applications, you can choose which ones you want to run.