The larger companies may also have been shorted but the bank's shareholdings may not have reached the 5% threshold, or they already owned the shares and only shorted a portion of them (via some internal transfer mechanism - not sure how this might work, but US banks are already into our goldies).
One non-sinister explanation for the banks shorting the goldies could be that they are acting on behalf of overseas hedge funds who are long physical gold and the shorting of the miners worldwide is a hedge against a lower USD POG.
