It's daft really but i installed WP in a directory called wordpress, styled it how i wanted and changed a few bits of text in the php then decided i wanted it in the root directory.
I guess it's something to do with the uri's but as far as i can tell it shouldn't be.
I did change some re-directs from login and logout to go the root index.php instead of the admin panel because i'm using angsumans ac-authentication plugin.
Any help would be greatly appreciated.
(using a tweaked version of the classic theme)