If you have a knockd configuration with a start_command and a stop_command, the stop_command does not get executed if you shutdown the knockd server.
stop_command should executed on cmd_timeout OR knockd shutdown, otherwise leaving the system in an inconsistent state.

so runing /etc/init.d/knockd stop should trigger "stop_command" if and only if knockd is still waiting for a cmd_timeout.

that way you do not need to run a stop_command manually if you change your knockd.conf and restart your knockd server.

regards
janning