You will get this whenever more than one face occupy the same plane. If you want to show alternatives, you have to put the face (and edges) in a group and assign to a layer, put the conflicting alternate face in a group and assign to a different layer. Make the layer setup for each scene hide the ones you don't wish to see. (If that makes any sense.) You might group all the interior wall surfaces for each scene together.
Either erase or hide that portion of GE terrain that lies under your carpet, or raise the floor above the GE image. Is the floor really exactly at ground level? It may be that the interior scene you are showing doesn't need the GE image layer on at all.
If this is not the answer, please post a model file.