What started off as a filter issue has become somewhat of an interface issue. A few weeks or so ago, after doing an update of the plugin, I too was one of the crowd who had lost all my filters. I set them all up again (copy and paste via a saved file), but none of the filters have worked at all since then. I get alerts regular as clockwork, so the plugin is working from that regard. It's just a question of not being able to filter out cache files/directories, error_log files etc.
Then when I was checking out the screenshots for the plugin (from the downloads page) I saw that the screenshot for the main settings page for the plugin was very different from the settings page on my actual site.
Since I've discovered this I've deactivated and deleted the plugin from my site, then re-uploaded and activated a new install but the result is still the same old settings page as the one I had before. I was wondering if anyone had any ideas about this. All caching plugins have been deactivated by the way, so it's probably not a caching problem.