The internal web server of FREESCO is based on thttpd and it doesn't have nor require an httpd.conf. This tiny but powerful web server is controlled via command line switches.
Now, I'm pretty sure the iptotal package sets all the directory and file rights correctly, but like I've mentioned before you may have to tell the web server that /www/iptotal can contain CGI scripts, where these scripts are normally expected in /www/cgi.
(iptotal was my very first FREESCO package (back in 027 days) and the decision to use a directory other then /www/cgi hunts me to this day

)
The question to Lightning is, what CGI pattern is used in thttpd in FREESCO?
You can set a different pattern by providing a CGI pattern in the command line that start thttpd (see rc_httpd script).
See the thttpd man page for the syntax.
I will also try iptotal on a FREESCO 0.3.8 test box and see if I can reproduce the problem.