Forum Moderators: DixonJones
From an SEO point of view it would be much better for you to only have one version of your home page. I would be looking to 301 redirect any requests for /index.php to /. You could do that quite easily using .htaccess.
And that would also fix your analytics issue!
RewriteCond %{HTTP_HOST} ^domain\.com
RewriteRule ^(.*)$ [domain.com...] [R=permanent,L]
RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php\ HTTP/
RewriteRule ^index\.php$ [domain.com...] [R=301,L]
Its always best not to have two instances because Google will need to prioritise one of them or maybe put it in the supplementary index