Remote file template not updating on website

Hello I am very very new to dreamweaver and have been handed a website that I have to maintain and make changes to.
The website uses a template called index with further nested templates as shown
The index template contains the code for the Menu Bar and footer and although I have been able to make other updates and changes I am finding that any changes to the code on this template do not show up on the site. The strange thing is that both the local and remote code has updated as I would like it is just the website itself that is not changing. When I view the website source code it is different to the remote file code. I assume that the link between the two is somehow broken but I do not know how to fix it. Is there a trick to fixing such a problem or am I wrong about this being the problem?
Here is the remote file code which is that same as the local code - I have out the code that is not updating in bold and underlined it:
<body>
<div class="container">
  <div class="header">
    <div id="header_top">
      <div id="text_only"><a href="http://www.genesi-fp7.eu/betsie/parser.pl">Text-only</a> </div>
       <div id="admin"><a href="../admin/index.php">admin</a> </div>
      <div id="search"><a href="../webpages/search/search.html">search</a></div>
      <div id="header_middle">
        <div id="logo_left"><img src="../images/500px-Flag_of_Europe.svg.png" alt="European Union" width="167" height="111" border="0" /></div>
        <div id="logo_middle"><img src="../images/Genesi_Logo.png" alt="GENESI" width="620" height="111" border="0" /></div>
        <div id="logo_right"><a href="http://cordis.europa.eu/home_en.html"><img src="../images/fp7.png" alt="Seventh Framework Programme" width="154" height="111" border="0" /></a></div>
      </div>
      <div id="header_bottom">
        <ul id="MainMenu" class="MenuBarHorizontal">
          <li><a href="../index.html">home</a> </li>
          <li><a href="../webpages/news/news.php">news</a></li>
<li><a href="../webpages/programme/programme_wp1.html">programme</a></li>
<li><a href="../webpages/consortium/consortium_0.html">consortium</a></li>
<li><a href="../webpages/downloads/downloads.php">downloads</a></li>
<li><a href="../webpages/links/links.html">links</a></li>
          <li><a href="../webpages/contact/contact.html">Contact</a></li>
        </ul>
      </div>
    </div>
    <!-- end .header --></div>
  <!-- TemplateBeginEditable name="mainSection" -->
  <div class="mainSection">
    <h1>here is the main section </h1>
  </div>
  <!-- TemplateEndEditable -->
  <div class="footer">
    <div id="footer_top">This project is co-financed by the <a href="http://ec.europa.eu/index_en.htm">European Commission</a> and made possible within the <a href="http://cordis.europa.eu/fp7/home_en.html">VII Framework Programme</a></div>
    <div id="footer_middle">Page maintained by <a href="mailto:[email protected]">Molly Buckingham</a> &middot; Last update: <!-- #BeginDate format:En2 -->03-Apr-2013<!-- #EndDate -->
    </div>
    <div id="footer_bottom">
      <div>&copy; 2012 <a href="../webpages/consortium/consortium_1.html">G.EN.ESI Consortium</a> &middot; <a href="../webpages/footer/Disclaimer.html">Disclaimer</a> &middot; <a href="../webpages/footer/privacy_notice.html">Privacy Statement</a></div>
    </div>
    <!-- end .footer --></div>
And here is the source code from the website - again the code is underlined and in bold
<!--[if lte IE 7]>
<style>
.content { margin-right: -1px; } /* this 1px negative margin can be placed on any of the columns in this layout with the same corrective effect. */
ul.nav a { zoom: 1; }  /* the zoom property gives IE the hasLayout trigger it needs to correct extra whiltespace between the links */
</style>
<![endif]-->
<!-- InstanceEndEditable -->
</head>
<body>
<div class="container">
  <div class="header">
    <div id="header_top">
      <div id="text_only"><a href="http://www.genesi-fp7.eu/betsie/parser.pl">Text-only</a> </div>
       <div id="admin"><a href="../../admin/index.php">admin</a> </div>
      <div id="search"><a href="../search/search.html">search</a></div>
      <div id="header_middle">
        <div id="logo_left"><img src="../../images/500px-Flag_of_Europe.svg.png" alt="European Union" width="167" height="111" border="0" /></div>
        <div id="logo_middle"><img src="../../images/Genesi_Logo.png" alt="GENESI" width="620" height="111" border="0" /></div>
        <div id="logo_right"><a href="http://cordis.europa.eu/home_en.html"><img src="../../images/fp7.png" alt="Seventh Framework Programme" width="154" height="111" border="0" /></a></div>
      </div>
      <div id="header_bottom">
        <ul id="MainMenu" class="MenuBarHorizontal">
          <li><a href="../../index.html">home</a> </li>
          <li><a href="../news/news.php">news</a></li>
<li><a href="../programme/programme_wp1.html">programme</a></li>
<li><a href="consortium_1.html">consortium</a></li>
<li><a href="../downloads/downloads.php">downloads</a></li>
<li><a href="../links/links.html">links</a></li>
          <li><a href="../contact/contact.html">Contact</a></li>
        </ul>
      </div>
    </div>
    <!-- end .header --></div>
  <div class="mainSection">
    <div class="SubMenuBar">
      <ul id="SubMenu" class="MenuBarVertical">
         <li><a href="consortium_1.html">Universit&agrave; Politecnica Delle Marche</a></li>
      <li><a href="consortium_2.html">Granta Design Ltd</a></li>
      <li><a href="consortium_3.html">Faber s.p.a.</a></li>
      <li><a href="consortium_4.html">Sibuet Environnement</a></li>
      <li><a href="consortium_5.html">Bonfiglioli Vectron Gmbh</a></li>
      <li><a href="consortium_6.html">ENEA</a></li>
      <li><a href="consortium_7.html">University of Bath</a></li>
      <li><a href="consortium_8.html">Grenoble Institute of Technology</a></li>
      </ul>
    </div>
    <!-- InstanceBeginEditable name="content" -->
    <div class="content">
      <h1><strong>The Università Politecnica delle Marche</strong></h1>
      <p><img src="../../images/delle_Marche.jpg" alt="The Università Politecnica delle Marche" width="142" height="142" />The Università Politecnica delle Marche(UNIVPM)  is situated in the Marche Region (area of  Ancona) that is the one of most important European industrial districts related  to the household appliances, in fact many European leader companies such as  Indesit , Elica, Ariston TG, Faber, and many others, have their headquarters  there. Thanks to this geographical position UNIVPM has many collaborations with  these companies and it has matured a vast skill on research topics related to  the household appliances field. UNIVPM has 5 faculties, 550 professors (the  largest is the Engineering Faculty with 180 professors), 12 technical Departments  and 17,000 students; it participates to 23 academic spin-off. The central administration  of UNIVPM has a management department which gives support to technical departments  in European project set up, negotiation and administration of the grant  agreement, draft and negotiation of the consortium agreement as well as project  financial reporting. In this project will be involved the Department of  Mechanics that has a remarkable experience on European Projects since it has  been coordinator of 6th and 7th FP projects and it is involved in 9 active  European projects.  In particular, UNIVPM  coordinates the G.EN.ESI project from an administrative and technical point of  view.</p>
      <p>The scientific contact at the Università Politecnica delle Marche for the G.EN.ESI  project is Prof. Michele Germani. </p>
    </div>
    <!-- InstanceEndEditable --></div>
      <script type="text/javascript">
var MenuBar2 = new Spry.Widget.MenuBar("SubMenu", {imgRight:"../SpryAssets/SpryMenuBarRightHover.gif"});
  </script>
  <div class="footer">
    <div id="footer_top">This project is co-financed by the <a href="http://ec.europa.eu/index_en.htm">European Commission</a> and made possible within the <a href="http://cordis.europa.eu/fp7/home_en.html">VII Framework Programme</a></div>
    <div id="footer_middle">Page maintained by <a href="mailto:[email protected]">Chunlei Li</a> &middot; Last update: <!-- #BeginDate format:En2 -->25-Apr-2012<!-- #EndDate -->
    </div>
    <div id="footer_bottom">
      <div>&copy; 2012 <a href="consortium_1.html">G.EN.ESI Consortium</a> &middot; <a href="../footer/Disclaimer.html">Disclaimer</a> &middot; <a href="../footer/privacy_notice.html">Privacy Statement</a></div>
    </div>
    <!-- end .footer --></div>
  <!-- end .container --></div>
<script type="text/javascript">
var MenuBar1 = new Spry.Widget.MenuBar("MainMenu", {imgDown:"SpryAssets/SpryMenuBarDownHover.gif", imgRight:"SpryAssets/SpryMenuBarRightHover.gif"});
</script>
</body>
<!-- InstanceEnd --></html>
Thank you in advance for your help

Jon Fritz that did actually work for some of the pages but not others. I upadted each invidivual page, except the main page as I have not finished the content and now some of the pages are acting strangely.
Here is the website http://www.genesi-fp7.eu/index.html
As you can see every page except the 'Contacts' and 'Links' page is now reading the correct code when you click on the 'Consortium' tab. The strange thing however is that the footer has updated on the 'Links' page suggesting that this part of the template has updated. Both these pages are based on the Index-misc nested template. The code is copied here:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"><!-- InstanceBegin template="/Templates/index.dwt" codeOutsideHTMLIsLocked="false" -->
<head>
<link href="../styles/genesi.css" rel="stylesheet" type="text/css" />
<script src="../SpryAssets/SpryMenuBar.js" type="text/javascript"></script>
<link href="../SpryAssets/MainMenu.css" rel="stylesheet" type="text/css" />
<link href="../SpryAssets/SubMenu.css" rel="stylesheet" type="text/css" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="google-site-verification" content="3L2ZN1aLnNO1X__brL1UzpHsgkiL7NdjWT8oJnAxF64" />
<!-- InstanceBeginEditable name="doctitle" -->
<title>G.EN.ESI</title>
<!-- InstanceEndEditable -->
<!--[if lte IE 7]>
<style>
.content { margin-right: -1px; } /* this 1px negative margin can be placed on any of the columns in this layout with the same corrective effect. */
ul.nav a { zoom: 1; }  /* the zoom property gives IE the hasLayout trigger it needs to correct extra whiltespace between the links */
</style>
<![endif]-->
<!-- InstanceBeginEditable name="head" -->
<!-- TemplateBeginEditable name="head" -->
<!-- TemplateEndEditable -->
<!-- InstanceEndEditable -->
</head>
<body>
<div class="container">
  <div class="header">
    <div id="header_top">
      <div id="text_only"><a href="http://www.genesi-fp7.eu/betsie/parser.pl">Text-only</a> </div>
       <div id="admin"><a href="../admin/index.php">admin</a> </div>
      <div id="search"><a href="../webpages/search/search.html">search</a></div>
      <div id="header_middle">
        <div id="logo_left"><img src="../images/500px-Flag_of_Europe.svg.png" alt="European Union" width="167" height="111" border="0" /></div>
        <div id="logo_middle"><img src="../images/Genesi_Logo.png" alt="GENESI" width="620" height="111" border="0" /></div>
        <div id="logo_right"><a href="http://cordis.europa.eu/home_en.html"><img src="../images/fp7.png" alt="Seventh Framework Programme" width="154" height="111" border="0" /></a></div>
      </div>
      <div id="header_bottom">
        <ul id="MainMenu" class="MenuBarHorizontal">
          <li><a href="../index.html">home</a> </li>
          <li><a href="../webpages/news/news.php">news</a></li>
<li><a href="../webpages/programme/programme_wp1.html">programme</a></li>
<li><a href="../webpages/consortium/consortium_0.html">consortium</a></li>
<li><a href="../webpages/downloads/downloads.php">downloads</a></li>
<li><a href="../webpages/links/links.html">links</a></li>
          <li><a href="../webpages/contact/contact.html">Contact</a></li>
        </ul>
      </div>
    </div>
    <!-- end .header --></div>
  <!-- InstanceBeginEditable name="mainSection" -->
  <div class="mainSection">
    <div class="SubMenuBar"><!-- TemplateBeginEditable name="subMenu" -->
      <ul id="SubMenu" class="MenuBarVertical">
        <li><a href="#">MISC</a></li>
      </ul>
    <!-- TemplateEndEditable --></div>
    <!-- TemplateBeginEditable name="content" -->
    <div class="content">
      <h1>Introduction to the G.EN.ESI Project</h1>
      <p>The sustainability of industrial products, particularly  household appliances, is an important issue today.  Energy consumption in the  residential/domestic sector is about 20% of world consumption, and associated  greenhouse gas emissions exceed 35%.   Household appliances contribute greatly to these values and thus require  particular attention as far as sustainability is concerned.</p>
      <p>It is well known that decisions taken during the early  design of products are very important in determining total product cost.  It is possible to hypothesize the same for  environmental impacts – i.e. the sustainability of a product is largely  determined during the early design stage. In order to allow designers to make  well-informed decisions, new design methods and tools are needed to provide the  basis for determining the degree of sustainability of a given product or  process.  Many eco-design procedures and  tools have been developed but they are often far from a practical day-by-day  application in company engineering departments, and they are not well  integrated with computer-aided design tools.   This project wants to make up for this limitation and to develop an eco-design  methodology (called G.EN.ESI) and a related software design tool (called the  G.EN.ESI platform) able to help product designers in ecological design choices,  without losing sight of cost and typical practicalities of industry. The  software platform will propose a guided process towards eco-design among  several design choices based on the different scenarios of product lifecycle.  The proposed approach will be applied to the household appliance field but it  can be easily extended to other mechatronic products.</p>
      <p>The project started in February 2012 and will continue until  January 2015.</p>
    </div>
    <!-- TemplateEndEditable --></div>
      <script type="text/javascript">
var MenuBar2 = new Spry.Widget.MenuBar("SubMenu", {imgRight:"../SpryAssets/SpryMenuBarRightHover.gif"});
  </script>
  <!-- InstanceEndEditable -->
  <div class="footer">
    <div id="footer_top">This project is co-financed by the <a href="http://ec.europa.eu/index_en.htm">European Commission</a> and made possible within the <a href="http://cordis.europa.eu/fp7/home_en.html">VII Framework Programme</a></div>
    <div id="footer_middle">Page maintained by <a href="mailto:[email protected]">Molly Buckingham</a> &middot; Last update: <!-- #BeginDate format:En2 -->03-Apr-2013<!-- #EndDate -->
    </div>
    <div id="footer_bottom">
      <div>&copy; 2012 <a href="../webpages/consortium/consortium_1.html">G.EN.ESI Consortium</a> &middot; <a href="../webpages/footer/Disclaimer.html">Disclaimer</a> &middot; <a href="../webpages/footer/privacy_notice.html">Privacy Statement</a></div>
    </div>
    <!-- end .footer --></div>
  <!-- end .container --></div>
<script type="text/javascript">
var MenuBar1 = new Spry.Widget.MenuBar("MainMenu", {imgDown:"SpryAssets/SpryMenuBarDownHover.gif", imgRight:"SpryAssets/SpryMenuBarRightHover.gif"});
</script>
</body>
<!-- InstanceEnd --></html>
Murray do you suggest that I try and get rid of the nested templates or am I biting off more than I can chew after two days of self training?
Thank you

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    ==================
    http://www.dreamweavermx-templates.com
    - Template Triage!
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    http://www.macromedia.com/support/search/
    - Macromedia (MM) Technotes
    ==================
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