"Startup Applications" not working
Solution 1:
Commands, especially those related to keyboard, mouse, and touchpad settings, or xrandr commands, often need the desktop to be fully loaded. If you run them simply at login (using Startup Applications), they often run too soon and break.
Therefore, you need to introduce a little time break before your actual command runs. Use the following command instead to add to Startup Applications:
/bin/bash -c "sleep 15 && xmodmap /home/seph/Code/Ubuntu\ Scripts/Xmodmap"
Open the dash → Startup Applications → Add, and add the command.
That should do the trick.