My navigation menu on header looks like this:

<ul id="nav">
                <li id="home">
                   <a class="mainmenu" href="#">Link1</a>                    
                </li>

                <li>
                   <a class="mainmenu" href="#">Link2</a>                    
                </li>


            </ul>

and the same markup is used for the footer section and it's not working. I have also a file called jscript.js which contains all the javascript for the website, and I found this variable:

var navTarget = "ul#nav li a" //menu link to target 

Also, if I remove for example the markup in the header sections the footer will work. I've tried also to use .nav instead of #nav and I have the same problem.

The navigation menu is controlled by javascript, I don't post the code here because it's huge, for better understanding of how the navigation menu works look here