in apache (both 1.3.9-8 and 1.3.9-4) in httpd.conf the line ServerRoot /etc/httpd is AFTER the apache module sections and in this case apache try to find the modules in /usr/modules/ even if there is a link in /etc/httpd/modules -> ../../usr/lib/apache/
I'm pretty sure you're looking at one of your old config files, and _not_ the one that we currently ship with apache. As of at least 1.3.9-8, ServerRoot directive is most definitely before the AddModule directives.