You have a thin film that's already semi-transparent. If you punch more holes into the film, do you expect more light to get through? You would, wouldn't you? That's not what happened here!
Toward this end, researchers from the University of Stuttgart in Germany laid very thin films of gold onto pieces of glass and then used ion beams to etch the film with holes arranged in a regular, square array. These holes were smaller than the wavelength of light and, despite being so tiny, are just the kind of openings that have been shown to let light through the thicker, opaque film used in the 1998 experiment. But in the new experiment, the gold film was so thin--only 20 nanometers--that light could already shine through it. And surprisingly, less light went through the holey gold than through the original semitransparent film.
You have to read the rest of the article (and maybe even the paper) to find out why. This, btw, is another example of some of the most fascinating results out of condensed matter.