Thanks lucy24 I have the following.
CentOS RHEL 6 running Apache 2.2.15 and php 5.3.3
I have everything running as virtual domains with no references to DocumentRoot anywhere except in the Virtual declarations.
I have been running successfully on my own static ip and servers using www.example.net for over 2 years. Things only got hinky when I introduced sub-directories / sub-domains into DocumentRoot.
An example of a couple of my virtual declarations
My main server site.
<VirtualHost *:80>
DocumentRoot "/var/www/html"
ServerName www.example.net
ServerAlias www.example.net
ErrorLog /var/www/html/example-2/logs/example_error_log.txt
LogLevel debug
</VirtualHost>
<VirtualHost *:80>
DocumentRoot /var/www/html/example-2
ServerName example-2.net
ServerAlias *.example-2.net
ErrorLog /var/www/html/example-2/logs/example-2_error_log.txt
LogLevel warn
</VirtualHost>
<VirtualHost *:80>
ServerName example-2.example.net
ServerAlias example-2.net
DocumentRoot /var/www/html/example-2
ErrorLog /var/www/html/example-2/logs/example-2_error_log.txt
LogLevel warn
</VirtualHost>
The problem is that the sub-directories / sub-domains all sitemap as frames w3c and other sitemap utilies all report the same thing. This is considered not Search Engine Optimized.
Hope that was enough to whet your whistle and hopefully it explains what happened.
Once again thanks for your time.
[edited by: tedster at 2:40 am (utc) on Jan 24, 2012]