While it's possible that there may be an issue with paths, I think it's secondary. The problem I see immediately upon scanning your code is that you are referring to DOM ID's of elements that do not exist. When you have an element with an id of "XYZ" and you add the runat="server" attribute to this element, then you can no longer rely on that element's DOM ID being "XYZ" any more. This is because the DOM ID is dynamically created by the ASP.net engine based on the hierarchical location of that element within all other server-rendered HTML elements.

The correct way to obtain a handle on such elements is to use the server-side .ClientID property. Your JS needs to be modified so it reads like this:

function showLayer(lyr)
{
    var eId = "";
    switch(lyr)
   {
         case "contactus" : eId = "<%= contactus.ClientID %>"; break;
         case "portfolio" : eId = "<%= portfolio.ClientID %>"; break;
   } 

   hideLayer(currentLayer);
   document.getElementById(eId).style.visibility = 'visible';
   currentLayer = eId;
}

Nik