Everything was ok until we updated our instaltion of WP to version 3.0. Let me explain the problem.
Our WP files are on a subfolder that we called "cms". The index.php is outside this folder and doesn't contain anyting because we didn't want to change our Index.htm file (that has a decent page rank, after 9 years of being online).
We are using a plugin called WP-CMS because we use WP more as a CMS than a bloging platform (although we have a blog too). Most of our pages are like that: pages instead of blogposts.
So far the mod rewrite did a good job by pointing the articles to their categories with URLs like http://www.ourwebsite.com/services/service1/index.htm
However, since the shortlinks implementation, all the pages (more than 600) include at the head section a link like that: http://www.ourwebsite.com/?p=3053 and when you click on that link (which is exposed at our sitemap), they all point to the index.htm which is the website home page! Hundreds of different URLs pointing to the same single page, can make google to bann us because of duplicating content.
I was not able to find a way to remove the permalink that is on the head section:
<meta name="generator" content="WordPress 3.0" />
<link rel='shortlink' href='http://www.ourwebsite.com/?p=3053' />
What can we do? Should we move the WP installation to the root of the website? How can we prevent this link rel for being there?
Anybody has an idea about where could be the problem?