This issue has been resolved.
www.
mydomain.com & www.
mydomain/index.php are regarded by Googlebot as 2 completely seperate URLs.
As I expected the 2 URLs have been indexed at different times.
www.
mydomain.com was last visited by Googlebot on Aug 14 when this page was still under construction.
www.
mydomain.com/index.php was last visited on Sep 29.
The best way to check the last date any page was indexed by using the "cache:" in the Google search.
This was probably caused by Googlebot finding links to www.
mydomain.com/index.php in the past month & not to www.
mydomain.com
If you have paid for .htaccess support on 110mb this can be solved with a simple redirect requests for index.php to the root:
Options +FollowSymLinks
RewriteEngine on
RewriteCond %{THE_REQUEST} ^.*/index.php
RewriteRule ^(.*)index.php$ http://www.mydomain.com/$1 [R=301,L]
Replace
http://www.
mydomain.com with the URL of your site.