I create a new layer in the Layer Properties Manager. Once I hit 'apply' it disappears. Then, when I create a new layer with the same layer name, it says it already exists. But I can't find the layers anywhere! Using:Autocad Architecture 2009

Maybe you've got an active layer status filter, e.g. "layers in use" wichs means Layer Properties Manager will only show layers containing objects. Take a look at Layer Manager to see if there is an active filter. If so, make current "All layers" filter, wich shows every layer in the drawing: those containing objects and those empty.