If you really removed shorewall from your runlevel (rc-update del shorewall
default) try this:
rm /var/lib/iptables/rules-save

i have removed shorewall from my runlevels and added iptables

Did you do a /etc/init.d/iptables save by any chance?  That's the only
thing I can think of.


the way i have applied my rules is as follows

first i load them with my generated script
then i invoke /etc/init.d/iptables save
and to be sure i do an /etc/init.d/iptables restart
iptables -L, iptables -L -t nat, iptables -L -t mangle show me my new rules
when i look in /var/lib/iptables/rules-save i also see my new rules
when i issue /etc/init.d/net.eth1 restart iptables -L, iptables -L -t
nat, iptables -L -t mangle show me the old rules from shorewall
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