Well you are trying to reinvent the wheel. Managing spam by simple filtering on keywords is hard to do well and spammers don't make life easy by using distinctive words. Anyhow, where are the messages after your filter has run? I'm not sure, but if a filter marking a message as Junk is treated as if you had set it by hand, then the message might be moved silently to your Junk folder, where the filter has probably lost sight of it. I don't think you can subvert the "new messages" alert, because downloading a message to the Inbox is a pre-condition for junk assessment. That is, for the filter to be able to work with a message, it must have the message where it can access the message's contents, and that means the message needs to be in your Inbox. And if a filter marks a message as Junk, it doesn't actually train the Junk controls, so this action in your filter is largely futile. It will leave a visible flag that tells ''you'' it is Junk, but Thunderbird doesn't act on it. To get filters that do invoke training, you'll need the FilterQuilla add-on. This allows the addition of a "Train as Junk" action to your filters. My first step would be to remove the "Mark as Junk" action. If everything else works, this labelling as Junk doesn't matter because the message ends up deleted.