The problem was with the DNNMenuNavigationProvider. I edited the skin file and change the menu provider over to the DDRMenuNavigationProvider.

I also had to take two lines of code from the original dark night skin in the register section and place them at the top of the skin file to register the DDRMenuNavigationProvider. These are changes that I needed to add to the register section::

<%@ Register TagPrefix="dnn" Namespace="DotNetNuke.Web.DDRMenu.TemplateEngine" Assembly="DotNetNuke.Web.DDRMenu" %>
<%@ Register TagPrefix="dnn" TagName="MENU" src="~/DesktopModules/DDRMenu/Menu.ascx" %>

Just check to make sure that they are not already there so you don't add them twice.
Then I needed to edit this line in the code itself in the skin file::

DNNMenuNavigationProvider" IndicateChildren="false" ControlOrientation="Horizontal" CSSControl="menuBar" />

To look like this:

DDRMenuNavigationProvider" IndicateChildren="false" ControlOrientation="Horizontal" CSSControl="menuBar" />

And that was it everything started to work fine again.

You will need to do this for every skin file you use on your pages so if you have different skin files on different pages you will need to edit each skin file you are using.