We have not known Emmeslink to fail to report a missing site, but for reasons not yet clear, a small fraction of sites periodically incorrectly report a page as "Not Found". For this reason, Emmeslink version 0.3 includes a button "Browse questionable links".
Pressing the "Browse questionable links" button causes your default browser to be called with a page that lists all the different links that were reported as quesionable, so you can re-check for their validity using the browser.