Just installed POPFile following a write in an IET article. Very nice but...
Clearly I just ran into this problem. All the rules seemed correctly configured EXCEPT. I had added all my Outlook Contacts addresses to the SPAM rule so that they were ALWAYS ALLOWED. One of the addresses in my contacts list was myself. Many SPAM messages spoof the "From" to include your own email address. Thus my SPAM rule failed to work until I removed my own email address from the list of allowed senders.
I suggest a brief addition to your troubleshooting file to alert people to this issue. (I realize its not something that POPFile can do anything about except warn us.)