When you say navigation list, where are you referring?

Strangely it works now, probably a cache issue...

Anyway, I was referring to the Navigation Group dropdown (in the top right corner) of the /fuel/navigation page.

Quickly another question: is there a way to get the location of the current page (not the URI)? I would like to add a canonical link for each page in the header.

Sorry for the troubles and thanks!

CodeIgniter has a current_url() function that sounds like what you need. For a URI, you can use the FUEL function uri_path().

My problem is that my client does not really make a difference between mysite.com/test and mysite.com/Test but Google in fact consider it as 2 different urls, this creates duplicate content.
I thought of the canonical link as a solution but I would need the actual location as saved in the DB to do that.

To query the pages_model, you can do the following:
$CI =& get_instance();
$CI->load->module_model(FUEL_FOLDER, 'pages_model');
$location = uri_path();
$page = $CI->pages_model->find_by_location($location);

However, find_by_location is case sensitive and "Test" and "test" are considered different so you may need to check for both by running a strtolower() or ucfirst() function on the $location value.