Comment 1 for bug 1162176

Are you certain it is being ignored and not just overridden by something else? Try having your script echo something to a file to verify it's running.

For example, if you have a ~/.config/monitors.xml file, GNOME will set the monitors up according to the contents of that file. Check also if you have a system level monitors.xml.

Most xrandr commands can also be set via the /etc/X11/xorg.conf (or /etc/X11/xorg.conf.d). These settings will take effect as soon as X starts up, so would make your boot a tiny bit faster and cleaner.

xrandr commands can also be issued on a per-user basis such as in your ~/.gnomerc or other such startup files. But note that per-user settings will only take effect on login, and wouldn't affect the login screen. However, these are executed pretty late so would at least work around if gnome or something else is mucking with your settings.