index.php removal issues

[eluser]echo_boom[/eluser]
I found this previous forum post:
http://ellislab.com/forums/viewthread/155801/

I followed instructions within it and created .htaccess file:

Code:

RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$0 [PT,L]

The problem:
I have to MANUALLY remove the ‘index.php’ for the URL to look clean. When I just go to the root directory OR click on a link within the app----when CI figures out the URL by itself the index.php is still there.

How do I get index.php to be gone completely?