A partial fix would be to run the following bash commands. The reason I say partial is because I got the permissions from a different firewall that does not have Guardian installed on it, so it could not determine the correct permissions for any of those directories.
This was taken from the output of a perl script I threw together. It is NOT commented (sorry) but pretty straight forward. Simply gets the permissions and ownership from each directory (and parent directory) out of an array based on Matthias' research. I did NOT check to verify the permissions were not already set. The output is simply a list of commands to set permissions from one machine to the same as the permissions on another.
The originating script is temporarily stored at http://unixservertech.com/fixPermissions.pl That is a web site in progress. Feel free to download and run it on a machine that has Guardian (after looking at it and making sure I didn't do something stoopid). No guarantee it won't eat your firewall, but I ran it on a production machine, then ran the output on my test router and it appears to have worked. ====================================================== chown 0:0 /etc chmod 0755 /etc
chown 0:0 /etc/logrotate.d chmod 0755 /etc/logrotate.d
chown 0:0 /etc/rc.d chmod 0755 /etc/rc.d
chown 0:0 /etc/rc.d/init.d chmod 0755 /etc/rc.d/init.d
chown 0:0 /etc/rc.d/init.d/networking chmod 0755 /etc/rc.d/init.d/networking
chown 0:0 /etc/rc.d/init.d/networking/red.up chmod 0755 /etc/rc.d/init.d/networking/red.up
chown 0:0 /etc/rc.d/init.d/snort chmod 0754 /etc/rc.d/init.d/snort
chown 0:0 /etc/rc.d/rc0.d chmod 0755 /etc/rc.d/rc0.d
chown 0:0 /etc/rc.d/rc3.d chmod 0755 /etc/rc.d/rc3.d
chown 0:0 /etc/rc.d/rc6.d chmod 0755 /etc/rc.d/rc6.d
chown 0:0 /opt chmod 0755 /opt
chown 0:0 /opt/pakfire chmod 0755 /opt/pakfire
chown 0:0 /opt/pakfire/db chmod 0755 /opt/pakfire/db
chown 0:0 /opt/pakfire/db/installed chmod 0755 /opt/pakfire/db/installed
chown 0:0 /srv chmod 0755 /srv
chown 0:0 /srv/web chmod 0755 /srv/web
chown 0:0 /srv/web/ipfire chmod 0755 /srv/web/ipfire
chown 0:0 /srv/web/ipfire/cgi-bin chmod 0755 /srv/web/ipfire/cgi-bin
chown 0:0 /srv/web/ipfire/cgi-bin/ids.cgi chmod 0755 /srv/web/ipfire/cgi-bin/ids.cgi
chown 0:0 /usr chmod 0755 /usr
chown 0:0 /usr/bin chmod 0755 /usr/bin
chown 0:0 /usr/lib chmod 0755 /usr/lib
chown 0:0 /usr/lib/perl5 chmod 0755 /usr/lib/perl5
chown 0:0 /usr/lib/perl5/site_perl chmod 0755 /usr/lib/perl5/site_perl
chown 0:0 /usr/lib/perl5/site_perl/5.12.3 chmod 0755 /usr/lib/perl5/site_perl/5.12.3
chown 0:0 /usr/lib/perl5/site_perl/5.12.3/Net chmod 0755 /usr/lib/perl5/site_perl/5.12.3/Net
chown 0:0 /usr/lib/perl5/site_perl/5.12.3/i586-linux-thread-multi chmod 0755 /usr/lib/perl5/site_perl/5.12.3/i586-linux-thread-multi
chown 0:0 /usr/lib/perl5/site_perl/5.12.3/i586-linux-thread-multi/auto chmod 0755 /usr/lib/perl5/site_perl/5.12.3/i586-linux-thread-multi/auto
chown 0:0 /usr/sbin chmod 0755 /usr/sbin
chown 0:0 /var chmod 0755 /var
chown 0:0 /var/ipfire chmod 0755 /var/ipfire
chown 0:0 /var/ipfire/backup chmod 0755 /var/ipfire/backup
chown 0:0 /var/ipfire/backup/addons chmod 0755 /var/ipfire/backup/addons
chown 0:0 /var/ipfire/backup/addons/includes chmod 0755 /var/ipfire/backup/addons/includes
chown 0:0 /var/ipfire/langs chmod 0755 /var/ipfire/langs
chown 0:0 /var/ipfire/langs/de.pl chmod 0644 /var/ipfire/langs/de.pl
chown 0:0 /var/ipfire/langs/en.pl chmod 0644 /var/ipfire/langs/en.pl
chown 0:0 /var/ipfire/menu.d chmod 0755 /var/ipfire/menu.d
chown 0:0 /var/log chmod 0755 /var/log ======================================================