Issue with SEF URI's

[eluser]jostster[/eluser]
I followed the directions here http://ellislab.com/forums/viewthread/176636/ and am still having an issue. I have to have index.php in my url or else I will get the default_controller page. I have set my uri protocol to PATH_INFO and copy/pasted the .htaccess, however, it will not work unless I include index.php/path/to/goto into the uri.

I currently have a folder under my root directory which I am making this CI application to test it before it goes live.

mysite.com/ci/index.php

Here is the mysite.com/ci/.htaccess file

Code:

#<IfModule mod_rewrite.c>
#   RewriteEngine on
#    RewriteCond $1 !^(index\.php|images|css|js|robots\.txt)
#    RewriteRule ^(.*)$ /ci/index.php/$1 [L]
#</IfModule>

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /

    #Removes access to the system folder by users.
    #Additionally this will allow you to create a System.php controller,
    #previously this would not have been possible.
    #'system' can be replaced if you have renamed your system folder.
    RewriteCond %{REQUEST_URI} ^system.*
    RewriteRule ^(.*)$ ci/index.php?/$1 [L]

    #When your application folder isn't in the system folder
    #This snippet prevents user access to the application folder
    #Submitted by: Fabdrol
    #Rename 'application' to your applications folder name.
    RewriteCond %{REQUEST_URI} ^application.*
    RewriteRule ^(.*)$ ci/index.php?/$1 [L]

    #Checks to see if the user is attempting to access a valid file,
    #such as an image or css document, if this isn't true it sends the
    #request to index.php
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    #RewriteRule ^(.*)$ ci/index.php?/$1 [L]
    RewriteRule ^(.*)$ ci/index.php/$1 [L]
</IfModule>

<IfModule !mod_rewrite.c>
    # If we don't have mod_rewrite installed, all 404's
    # can be sent to index.php, and everything works as normal.
    # Submitted by: ElliotHaughin

    ErrorDocument 404 ci/index.php
</IfModule>

Here is my system/application/config/config.php file

Code:

$config['index_page'] = "";

$config['uri_protocol']    = "PATH_INFO";

$config['permitted_uri_chars'] = 'a-z 0-9~%.:_\?\=\#\&\-';//'a-z 0-9~%.:_\-';

$config['enable_query_strings'] = FALSE;

Here is my routes

Code:

#Clothing
$route['clothing'] = "products/index/clothing";
$route['clothing/(:any)'] = "products/index/clothing/$1";

#Sponsor
$route['sponsor'] = "products/index/sponsor";
$route['sponsor/(:any)'] = "products/index/sponsor/$1";

I will also need to pass a variable in clothing sometimes that will be like
mysite.com/clothing/shirts?men

Inside my products.php controller I have

Code:

function __construct()
    {
        parent::__construct();
        
        parse_str($_SERVER['QUERY_STRING'],$_GET);
    }