Having a similar problem to Gunnar. I can't see that I have another version of SpamS. running, but the Stats for SS do not indicate any messages going into Filtered Mail or changing the SS accuracy listing, but each manually marked Spam message does go into the Corpus count.
I have an other test installation on a separate machine, with the same filtering settings as far as I can tell, and it seems to be working OK with new messages increasing the Filtered Mail count. Puzzled. -merrill