John, when you configure you spam checks as system admin | Security | Antispam Administration, you can specify where the spam check(s) are: 1. enabled for filtering (these are run on messages in the spool); 2. enabled for incoming SMTP blocking; and, 3. enable for outgoing SMTP blocking.
As Joe Wolf commented above, if you have a message rejected due SMTP Spam blocking (as the case is above), it will never hit the spool and will not be archived. I hope this clarifies a little.