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With a bounce rate that low, do you by chance have multiple GA tracking scripts, or something that's triggering an event even if no one goes to another page? Look at the source code when you're in incognito mode, in case your CMS suppresses one of the GA codes when you're logged in as admin. [voice of experience and learning the hard way here!]

If you are using an Apache server, you should be able to redirect the index.php file to the root by editing the .htaccess file with the following lines - RewriteCond %{THE_REQUEST} ^./index.php RewriteRule ^(.)index.php$ http://www.mydomain.com/$1 [R=301,L] If you are using WordPress, there are several plugins available which will allow you to configure this automatically so you don't have to mess with the .htaccess file manually.