I have never seen that problem before. You said you were using ubuntu?
From a bare-metal install, all I ever had to do to enable LDAP was:
# sudo apt-get install apache2
# a2enmod authnz_ldap
# /etc/init.d/apache2 restart
Did you install Apache via apt-get or did you build everything manually?
From my experience, I've never had to configure httpd.conf to enable the modules for me as a2enmod does it for you. You could try removing your edits from this file then re-enabling the mods.
Inside the folder /etc/apache2/mods-enabled/ we will find all the enabled modules. Here we will find symlinks to the files from mods_available for all the enabled modules. Only the modules found in this folder will be enabled at run time.