Training will only happen when you reclassify a message.
In particular, POPFile will not learn anything when it classifies a message, it will not learn when a magnet is triggered, and it will not learn when you move a message in your mail client from one folder to another.
That means that POPFile will not learn behind your back. You must tell it (by reclassifying a message) that it made a mistake and only then will it learn something.