Great question — answering as the UphillTech team:
The init.d scripts aren't run on login, so it's normal that it doesn't run if you just log out and in. They only run on boot, or when changing runlevels. /etc/init.d is the right place if the settings are global (shared amongst all users) and need only be run on boot. For simple tasks you may instead want to add the commands to /etc/rc.local, which doesn't use the start/stop lifecycle of /etc/init.d scripts. If the settings should be applied only for a certain user or be applied on each login, the correct place is the relevant profile for your shell ( ~/.profile , ~/.bash_profile , ~/.bashrc , ...) or, probably more adequate if running a desktop environment, in the session startup programs...
Full answer by outlyer: https://unix.stackexchange.com/a/169488 (CC BY-SA 3.0).
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