Correct CSS not loading when using Nav but works when going through full sitemap

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Hi all,

I'm having the weirdest and most frustrating thing happen. I created a theme using fireworks, made into php etc, and uploaded to concrete5. I made a home.php, a default.php, a right.php, a full.php, and uploaded a main.css and a typography.css.

The home page loads both the main.css and typography.css fine, looks how I want.
I then added some other subpages. In edit mode they look how I want. If i go through full sitemap in the dashboard, they look how I want(correct CSS)

However, if I use autonav from the homepage to any of the other pages, they don't pull through the correct css.

In firebug it shows that it should be calling the correct css file but instead shows this

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html lang="en" xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
<title>Health Express :: </title>
<meta name="description" content="" />
<meta name="generator" content="concrete5 - 5.5.2.1" />
<script type="text/javascript">
var CCM_DISPATCHER_FILENAME = '/concrete5.5.2.1/concrete5.5.2.1/index.php';
var CCM_CID = 0;
var CCM_EDIT_MODE = false;
var CCM_ARRANGE_MODE = false;
var CCM_IMAGE_PATH = "/concrete5.5.2.1/concrete5.5.2.1/concrete/images";
var CCM_TOOLS_PATH = "/concrete5.5.2.1/concrete5.5.2.1/index.php/tools/required";
var CCM_BASE_URL = "http://localhost";



Can anyone help, its really driving me nuts!