при отключении network manager и установке конфигурации интерфейса eth0 вручками в /etc/network/interfaces в состояние iface eth0 inet static knockd при старте системы запускается.
$uname -a
Linux cit-debian-03 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
$ cat /etc/issue
Debian GNU/Linux 7 \n \l
$ dpkg-query --list network-manager | grep network-manager
ii network-manager 0.9.4.0-10 amd64 network management framework (daemon and userspace tools)
$ dpkg-query --list knockd | grep knockd
ii knockd 0.5-3 amd64 small port-knock daemon
# chkconfig --list | grep -E '(knockd|network-manager)'
knockd 0:off 1:off 2:on 3:on 4:on 5:on 6:off
network-manager 0:off 1:off 2:off 3:off 4:off 5:off 6:off
# ps aux | grep `cat /var/run/knockd.pid` | grep -v grep
root 2605 0.0 0.0 8312 4424 ? Ss 09:08 0:00 /usr/sbin/knockd -d
[FAIL] Starting Port-knock daemon: knockd failed (could not open eth0: eth0: that device is not up).