So after learning more about how CEGUI actually renders things I was able to get the samples correctly loading (I don't know how I was able to break the sample loading).
Turns out that CEGUI uses rtts to render things to and not just the main render window...
So now that I basically have made it use the whatever functionality is left in ViewPorts, it works.
Also now that I fixed the clearing problem it looks like I think it should look like.
The only problem is that I'm using ViewPorts, still. So I can't guarantee that the GUI actually ends up on top of everything.
What I think needs to be done is quite a large OgreRenderer overhaul using just a single Ogre scene where everything is located.
So that all the ViewPort and texture usage would be changed to Ogre objects (manual objects or something else) actually where scene objects for which Ogre would handle redrawing/ordering.
From what I've seen this would reduce things that the renderer would have to do since the scene can manage much of the shaders and custom matrices etc.
Making a pull request for the now working code.