If you use an email scanning proxy that has changed your email setting like some versions of Norton Antivirus, then POPFile won't work straight off the bat: the email proxy will grab them instead. You need to configure POPFile to talk to the email scanner. (If your virus scanner didn't change your email POP3 server setting then there is no need to follow these instructions).
(So, basically, emails get downloaded by the scanner, passed to POPFile, and then - finally - passed to your email program.)
Now, since different brands of email scanners work differently, we'll work like this:
Follow your manufacturer's instructions for this.
Head to the Web Interface's Configuration tab, and change your POP3 Listen Port to any similar number - we recommend 123. Click Apply.
( and possibly more. Todo: Check the Howtos section)
Reactivate your scanner (consult your scanner's manual) and it should automatcally set everything up for you. Mail should now be scanned and sorted.
Should you find anything in the documentation that is incomplete, unclear, outdated or just plain wrong, please let us know and leave a note in the Documentation Forum.