Some of the above code didn't post correctly. I am reposting with the missing code:

Here is what I have at the top of my Skin ascx file:
<%@ Control language="C#" AutoEventWireup="false" Explicit="True" Inherits="DotNetNuke.UI.Skins.Skin" %>
<%@ Register TagPrefix="dnn" TagName="SEARCH" Src="~/Admin/Skins/Search.ascx" %>
<%@ Register TagPrefix="dnn" TagName="LOGO" Src="~/Admin/Skins/Logo.ascx" %>
<%@ Register TagPrefix="dnn" TagName="USER" Src="~/Admin/Skins/User.ascx" %>
<%@ Register TagPrefix="dnn" TagName="LOGIN" Src="~/Admin/Skins/Login.ascx" %>
<%@ Register TagPrefix="dnn" TagName="BREADCRUMB" Src="~/Admin/Skins/BreadCrumb.ascx" %>
<%@ Register TagPrefix="dnn" TagName="COPYRIGHT" Src="~/Admin/Skins/Copyright.ascx" %>
<%@ Register TagPrefix="dnn" TagName="TEXT" Src="~/Admin/Skins/Text.ascx" %>
<%@ Register TagPrefix="dnn" TagName="JQUERY" Src="~/Admin/Skins/jQuery.ascx" %>
<%@ Register TagPrefix="dnn" TagName="META" Src="~/Admin/Skins/Meta.ascx" %>
<%@ Register TagPrefix="dnn" TagName="MENU" Src="~/DesktopModules/DDRMenu/Menu.ascx" %>
<%@ Register TagPrefix="dnn" Namespace="DotNetNuke.Web.Client.ClientResourceManagement" Assembly="DotNetNuke.Web.Client" %>

Then I have this down farther in my Skin ascx file:
 <!-- Start : SubMenu -->
<!--#include file = "includes/dept/dept-submenunav.ascx" -->
<!--// End : SubMenu -->

Then in my include dept-submenunav.ascx file I have:
<nav class="wssubmenu clearfix">
           <ul class="wssubmenu-list">
              <li class="wsli-submenu">
                   <div class="submenuheaderwrap">
                        <div class="submenuheader">
                           <ul>
                               <li><a href="<%= ((DotNetNuke.Entities.Tabs.TabInfo)PortalSettings.ActiveTab.BreadCrumbs[0]).FullUrl %>"><%= ((DotNetNuke.Entities.Tabs.TabInfo)PortalSettings.ActiveTab.BreadCrumbs[0]).TabName %></a></li>
                            </ul>
                        </div>
                    </div>
                   <div class="submenu-wrap clearfix">
                       <div class="submenu_full">
                           <div class="second-level-list">
                                <!-- ul submenu items -->
                                <dnn:MENU runat="server" menustyle="navs/sub-menu" NodeSelector="+0,0,2"/>
                               <!--// end ul submenu items -->
                            </div>
                        </div>
                   </div><!-- end submenu-div-->
                </li><!-- end li Parent-->
           </ul>
       </nav>

The Code is showing the Root Level Parent correctly on the page visually, but when I am in the DNN Admin mode, the code is causing issues. When I try to add a new module to a Content Pane it makes all the modules go to that one Content Pane no matter what other content pane they are currently in. 

The code is causing issues because it makes the div class="DNNAjaxPanel" disappear.

PLEASE TEST by adding the code below to a C# skin ascx file. Then login to DNN admin and try to add a few modules in different content panes and see what happens.
<a href="<%= ((DotNetNuke.Entities.Tabs.TabInfo)PortalSettings.ActiveTab.BreadCrumbs[0]).FullUrl %>"><%= ((DotNetNuke.Entities.Tabs.TabInfo)PortalSettings.ActiveTab.BreadCrumbs[0]).TabName %></a>

Then, use the Inspect Element feature of your browser and you will see that the div class="DNNAjaxPanel" has disappeared. If you Inspect Element of a Skin ascx page that doesn't have the code and you will see the div class="DNNAjaxPanel" is there.

Note: the div class="DNNAjaxPanel" is the div just above the div class="DNNEmptyPane dnnSortable dnnModuleManager ui-sortable"

Is this a issue or bug with DNN 9.1.1?

Thanks,
Craig