An Err message normally means that speaker cable is reversed. I think most modern receivers can handle this, but, the auto setup just lets know for your information that the wires might be reversed. On some speakers/setups it might give an err even with everything right. For instance, my last amp, a marantz sr8001 always gave an err for left speaker, even though everything was perfect.
To sum up, if you get an err during autocalibration and then have gone back and checked your speaker wire and your connections and everything looks ok, then I think it's safe enough to ignore the err message,.