There is a known bug that stops Redshift starting automatically in elementary and some other Ubuntu derivitaves due to geoclue conflicts on startup.
To work around this, you need to "hard code" your location into the startup command for Red Shift:
1. Just Google " lat long for <Your Location>"
2. Now we're going to create a Custom command to run at startup that will hardcode that location bypassing the geoclue error. To do this, Open Scratch and craft the following command:
gtk-redshift -l <LAT>:<LONG>
So in our example for Boise, we would type:
gtk-redshift -l 43.588709:-116.229978
3. Now go into Settings >> Applications >> Startup and add the command to load at Startup:
NOTE: With this command entered, it should work whether or not Autostart is checked in the Redshift notification menu.
5. Now reboot, and Red Shift should load on startup as intended!