Please find below the details for the .js file we had to edit to clear the Citrix cookie problem:
 
File Location: C:\inetpub\wwwroot\Citrix\XenApp\uk\app_data\clientscripts\cookies.js
 
Within that file you need to find the following block of text:
 
var cookie = name + "=" + value;
<%  // The cookie path appears to cause problems for the way NetScaler proxies cookies.
    // We do not use path with AG / NetScaler to improve compatibility with them.
    if(!AGEUtilities.isAGEIntegrationEnabled(wiContext.getConfiguration())) {
%>
    cookie = cookie + "; path=<%=wiContext.getWebAbstraction().getAbsoluteRequestDirectory()%>";
<% } %>
    document.cookie = cookie;
 
And within that block of text deleted the following line:
 
cookie = cookie + "; path=<%=wiContext.getWebAbstraction().getAbsoluteRequestDirectory()%>";