GET parameters won't work

[eluser]Mr. Pickle[/eluser]
Hi, I'm having a problem with GET parameters (query parameters).
Some external sites (like Google) add a GET parameter when linking to my site, but this is also done by several affiliate programs. For example:
http://www.mysite.com/?gclid=a-string-comes-here (Google)

When loading this URL I get:
404 Page Not Found
The page you requested was not found.
while loading http://www.mysite.com/ loads ok.

I know because of security reasons CI does not allow query parameters.
For other sites I have found a solution in:

1. Removing the ? from the htaccess rewriterule;
2. Set uri_protocol to PATH_INFO (instead of default AUTO);
3. Leaving the enable_query_strings to FALSE.

I have even got this working local for this project. But for some reason when publishing the code to my server it does not work anymore. Setting PATH_INFO results in having all my pages load the default controller (as if CI does not read the full url anymore)
Removing the ? from the htaccess also troubles it completely.

For info, the server runs on Ubuntu with Apache 2.2.8

At this moment I got back to default settings (and thus with a non-working site if query param is present)

My current .htaccess:

Code:

RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

RewriteRule ^(.*)$ index.php?/$1 [L]

My current config.php contains (only those applicable on this issue)

Code:

$config['index_page'] = "";

$config['uri_protocol']    = "AUTO";

$config['enable_query_strings'] = FALSE;