Can anyone give me any advise on why my store has a index.php ending to the store url? I have never seen this before and i am sure it cannot work for search engines. Even the admin url has a .php ending which i find very strange.
Depending on your .htaccess file, generally your site should not be showing the /index.php in the address bar.
Things to check might be:
1) redirects are enabled for your web server (apache or nginx).
2) SEO addon is installed and active
3) .htaccess file exists and is standard
Admin will always show [admin_index_file].php given that no SEO is performed in the admin area.