The problem with running an empty microwave is that it doesn't have anything inside to absorb the microwave energy. So a lot of that energy tends to get absorbed in the magnetron tube that's also the microwave source. It will overheat if that goes on very long. It sounds (smells) like you did a little of that, but since the microwave is still working ok, I wouldn't worry about it. Obviously it's good to avoid doing that again.
Mike W.
(published on 03/12/2014)