Not that this is a Perl problem per se . . .

Just having the startup/shutdown script in /etc/init.d isn't enough; it also needs to be symlink'd into the appropriate rc(runlevel).d directory (e.g. /etc/init.d/rc5.d for a typical X11-running machine). The easiest way to do this is provide suitable comments in your init.d script such that chkconfig knows how to handle it. See man chkconfig and specifically its section on "Runlevel Files" for more details.