I installed the demo of SpamSieve 2.5 and started the training process, but when it moved mail that was not Spam into my Inbox, it marked 14 messages as Unread, even though all of them were (and are) Read. No amount of opening each, or selecting them all and marking them as Read again changes that.
I tried updating to the 2.6.6 demo version but that changed nothing.
Yes, I saw that menu, but in 2.5 it only asks what folder I want the Spam to be put in, nothing else. But more to the point, I’ve been through every message in my Inbox and opened them all since it marked 14 as Unread; that count doesn’t change and there is no indicator by any message to show it as Unread.
Which mail program are you using? If you have Entourage, you may need to re-install the scripts after updating to 2.6.6. With recent versions of SpamSieve, one of the questions it asks will be whether to mark messages as unread when you train as good.
If the mailbox’s unread count is out of sync with the messages’ actual unread states, that’s an issue with your mail program, not SpamSieve. Perhaps its database needs to be rebuilt.