In /etc/httpd.conf there is a clause | <Location /> | ... | </Location> This statement has a higher priority than <Directory> directives. That's why widely used configurations like | <Directory "/home/*/public_html/cgi-bin"> | Options ExecCGI | </Directory> won't work anymore. I think you should move everything from <Location /> into the <Directory /> section and remove it entirely.
Changing it back for apache-1.3.12-23.