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[eluser]pigfox[/eluser]
My setup is standard.
My nav looks like:
<a href="index.php">Home</a> |
<a href="sites.php">Completed Sites</a> |

The link to to sites.php loads index.php.

In /config/config.php I have
$config['index_page'] = "index.php";

In /config/routes.php I have:
$route['sites'] = "sites";

In /controllers/sites.php

/views/sites.php exsits.

The .htaccess file looks like:

RewriteEngine on
RewriteCond $1 !^(index\.php|resources|robots\.txt)
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L,QSA]

Requesting sites.php loads index.php, the url says sites.php but index content loads.

Does anyone have a solution to this?

[eluser]2think[/eluser]
Have you tried removing index.php from your config[index_page] in config.php? That might be the fix.

[eluser]pigfox[/eluser]
I tried that, commenting out that line in config/config.php
//$config['index_page'] = "index.php";
Makes no difference, the problem remains.

[eluser]2think[/eluser]
I also remember sometimes in setup, my Virtual Host configurations needed a lot of options enabled, esp AllowOverride. Have you done so in your VirtualHost directory setup?

I guess you may have seen this wiki page but if not, here it is: http://codeigniter.com/wiki/mod_rewrite/

[eluser]pigfox[/eluser]
It seems to have been fixed.
The solution was /config/config.php
//$config['uri_protocol'] = "AUTO";
$config['uri_protocol'] = "REQUEST_URI";

[eluser]pigfox[/eluser]
Oops, forgot to say "Thank You!!"

[eluser]2think[/eluser]
Good to hear and you're welcome. However, the community spirit and helping of MANY Codeigniter users really set the pace.

There may be a dozen other apps and I've even used other languages but the community spirit of the Codeigniter community sets it above and beyond, at least in my opinion.

Glad you figured it out more or less on your own. Best wishes with the framework and community.