Help needed duplicate pages, description, metas

Hello rapidweavers,
I’ve been working a while with rapidweaver, which i consider a great tool to design wonderful websites.
Doing a check up for one of my websites i’m confronting with the following problem, almost every page i have is seen in webmaster tools as duplicate content, description, metas, etc.
I would like to mention that this problem is shown as follows:



It is not a index.html - index.php problem because i have checked.
Could this have something to do on how "file links are relative to: Page/Docroot/website address ?
Would canonical rel help me in this case?
Thank you all for suggesting a fix.

What tool?
The two links above are the same, the only difference in the URL’s is one has the full name (with index.php) the other defaults with just the directory name. Should be laoding the same page.

Hello, thanks for your reply.
Webmaster tools from google sees this root/ and root/index.php as duplicate apparently so at the HTML improvements option i get to see all my pages marked as duplicate content/ description/ metas