Remove index.php

[eluser]morph london[/eluser]
I have a website that uses a .htaccess file to remove the index.php. I goto www.mysite.com/admin/login/ and it works fine so the .htaccess is working. Now when I do a redirect using the built in function it directs to www.mysite.com/index.php/admin/login/. It obviously does not break the site, but I was just wondering how to remove it. My colleague is building a site exactly the same as mine and his does not do it. But we can not work out if hes changed a setting somewhere.

Thanks Alex