I’m having the same issue, only everything seems OK as far as the setup goes. SpamSieve rule was checked, rule was properly constructed, top of the list. Lots of spam getting thru to the inbox that used to be caught, repeatedly. Problem started after upgrade to Mavericks. Key commands to move messages to spam are really slow to react, so much so that I am tempted to hit the keys again. No good messages are going to Spam.
Please follow the instructions on this page, including “If you have spam messages in your inbox” and send the information via e-mail.
Please see this thread.
Thanks for sending the log file. The log shows that, for this copy of SpamSieve, almost all the messages that you’re training as spam were not ones that SpamSieve had seen. In other words, the SpamSieve rule was not applied to them. This could be because of a problem with the rule setup or because another computer or device marked the messages as read or moved them out of the inbox so that Mail did not auto-apply the rule.