When i check google webmaster tools i found that google saw two pages with duplicate title tags and meta descriptions. This should be normal sometimes (this does not mean that we should ignore it) but the mysterious part for me is that the two pages are the "/" and "index.php". Why happen that? Is possible the latest "/" counted as page for google (i don't believe google is so stupid)
Maybe you have it linked one time as /index.php and one time as / ? Also maybe it's a solution to location redirect automatically to one of them if the other is accessed that probably would also change the way google looks at them.
You can 301 redirect /index.php to http://www.yoursite.com - this will ensure all of your link juice goes to your home page.
added that on January 30 then the content analysis updated at January 31 and February 1 but the same "duplicate content" message. Do something wrong?