So … I’ve of course, upgraded to version 3.0. SpamSieve was on of the best pieces of software I’ve used in my life, and recommended to a lot of people.
Now I’m back to just having to flag all my individual spam e-mails, like it is 2010.
So not worth it …
Most likely you are encountering an Apple bug for which there is a workaround. Please see this page or send in a diagnostic report if you don’t think that sounds like the issue you are seeing.
SpamSieve 3.0.1b2 can now automatically filter new messages in the inbox that Mail failed to send to the Mail extension. So, in most cases, you no longer need to do anything to work around this Mail bug.