[eluser]talldarkmystere[/eluser]
If you're including your head as part of a sub-view that is then included in another template, be sure that you're using the TRUE flag to tell CI that it needs to process the sub template before passing it to the main one.
Code:
$headerdata['title'] = 'My Page Title';
$headerdata['css'] = 'mycssfile.css';
$data['head_content'] = $this->load->view('head_sub_template', $headerdata, TRUE);
$this->load->view('body_template', $data);
Without the TRUE flag, the content will still be passed, but it will be thrown into the top of the page.