Save IPTables rules

I'm not having any problem creating or saving the rules, I have them just the way I want.
My problem is that when I use:
iptables-save > /etc/sysconfig/iptables
There is something specific to the FreePBX Distro that I get a duplicate copy of the default rules. It appears there is some bash script that runs on startup that add the FreePBX Distro rules.
So what happens is I get:
Default rules
Some of my rules
The default rules again (because they are included in my file)

If I just remove the default from my list then they aren't in the right order. If I could remove the default rules from applying on boot I would be where I want to be.