However, most of the server-manager website is dead. I cannot view log files, modify users, add users, reboot or shutdown, add hosts, etc.
I too have the same problem after getting the following updates-
perl-CGI-Persistent.noarch               1.00-1.el4.rf          smeupdates      
perl-Compress-Raw-Zlib.i386              2.008-1.el4.rf         smeupdates      
perl-Compress-Zlib.noarch                2.008-1.el4.rf         smeupdates      
perl-Crypt-Cracklib.i386                 1.1-1.el4.rf           smeupdates      
perl-DBI.i386                            1.601-1.el4.rf         smeupdates      
perl-HTML-Tabulate.noarch                0.26-1.el4.rf          smeupdates      
perl-I18N-AcceptLanguage.noarch          1.04-1.el4.rf          smeupdates      
perl-IO-Compress-Base.noarch             2.008-1.el4.rf         smeupdates      
perl-IO-Compress-Zlib.noarch             2.008-1.el4.rf         smeupdates      
perl-IO-Zlib.noarch                      1.07-1.el4.rf          smeupdates      
perl-Mail-DKIM.noarch                    0.29-1.el4.rf          smeupdates      
perl-Quota.i386                          1.6.0-1.el4.rf         smeupdates      
perl-Text-Iconv.i386                     1.7-1.el4.rf           smeupdates      
So it would appear to be one or a combination of these causing the problem
Also I checked the server- manager httpd error logs
/var/log/httpd/admin_error_log. and found errors pointing to cgi perhaps you could check yours to see if you have similar errors.
Also since it looks like this is not a singular occurrence perhaps you should enter a bug for this.