I guess the problem you got comes from a CTRL-D called when the layer containing that object is not the one active.

Layer1 : empty (active)
Layer2 : PolyCube1 (inactive)

If you click on the polycube to select it and layer1 is still active
>> CTRL-D leads to this greenwired copy which is untextured.

Solution is, select object and layer relative to it, then call CTRL-D.
To drop the duplicated in another layer, right-click the target layer and choose "add selected objects".

Another solution is just selecting the object, then right-click a shader in the hypershade and choose the "assign material on selected"


Hope that helps a bit