Ubuntu – Order in startup application preferences

It sounds like a permission problem, you can try this (from a terminal):

sudo chown [username]:[username] -R ~/.config

If it doesn't help, try to start the "Startup Application Preferences" from a terminal using this command:

gnome-session-properties

You might see relevant error messages there. If the output looks useless to you, you might post it here.

Startup scripts, related to keyboard- or touchpad settings, or include wmctrl or xrandr commands often need "a little break" before running. If they run too early, before the desktop is fully loaded, they either break or "miss their target".

To solve that, you need to add:

/bin/bash -c "sleep 10 && /home/myuser/myscript.sh"

to your startup applications. Possibly you need to play a little with the sleep 10 value to optimize.

Note

Probably the script exists of only one or two commands, you could include them in your startup command, with the same syntax. That way you do not need a separate script.