I’ve had something similar to this happen before where I swore that LayOut was creating lines that weren’t in my original SketchUp scenes.
After closer investigation and inspection, the best way to say it is that LayOut does not add any additional viewports to your model. I would double-check your scenes in SketchUp. Is it possible you’ve got an extra viewport somewhere?
You can try deleting and re-running the scenes, or go back and re-load the ConDoc v4 – ARCHITECT.condoc file, and run the scenes again. This usually did the trick for me.