I have been having a really curious problem with several netfilter frontend gui's. (eg Knetfilter, although others have done the same thing.) on Mandrake 9.1 (straight from the distro kernel and modules)

What happens is that when you try and run the thing, it whinges about how iptables is not installed. The problem is that it blatently IS installed, because it's currently running as a service.

The errors vary, but they're all about "You don't have iptables support compiled into your kernel" or "you don't have iptables installed." Which again is complete rubbish.

Am I missing something blindingly obvious here?

I have never really been impressed with the "pre-packaged" netfilter tools on any distro. If you are looking for a GUI, try webmin, shorewall or fwbuilder. These actually do what they say they will.

Are you sure it is saying IPTABLES isn't installed? I have seen those error messages before but it was for IPCHAINS. Regardless go and check out guarddog for a GUI front end to IPTABLES.