Tente colocar o script em diferentes níveis de execução.
/etc/rc0.d - While system shuts down.
/etc/rcS.d - While system boots
/etc/rc1.d - Working as singel user (user specific on login)
/etc/rc2.d - Working as multiple users
/etc/rc3.d bis /etc/rc5.d - not used in ubuntu
/etc/rc6.d - While system restarts