I have a VPS (Virtuozzo) with cPanel installed. I notice that iptables running in the VPS had many DROP rules when I listed using iptables -nL command. So I flushed iptabled using "iptables -F" command and also "> /etc/sysconfig/iptables" command and restarted iptabled. When I try to list the rules it would show empty. However when I try to list after a few minutes it is showing the same old rules with many DROP rules yet again! Is there anyway to remove the rules completely?
If what you say is true, then there is something else entering the rules. Before you can control IPtables yourself, you need to figure out what is managing them, and disable that, then if you clear out the IPtables, restart, and they are still clear, they should stay clear.