I can see the problem. The plugin adds the footer after the article has been rendered, which includes the "Next", etc. buttons if required. This means that it isn't the same as adding text to the bottom of an article exactly.
In the case of your site, the article is displayed in a table, but due to the way the template is rendered, the plugin can only add text after the table code.
I guess this is essentially a limitation of the plugin at the moment. I can look into it to see if there are any other options for adding the footer earlier, but I am not sure there are - not without fundamental redesign of the plugin, anyway.