I’ve noticed that Apple Mail is no longer marking a newly arrived message in the Inbox message list as read (removing the unread mark) after I’ve opened the message to read it and closed it again. I have to switch away to another mailbox and come back again, to get the updating to happen. But this is true only for new messages, i.e. those that SpamSieve has examined automatically on receipt. Is there any chance that SpamSieve is helping to cause this behavior?
I don’t think so, because SpamSieve doesn’t mark any messages as read or unread. It sounds like your Mail database may be damaged; I suggest doing a complete rebuild.
This is likely a known synchronization bug, nothing to do with SpamSieve. Is your Inbox hosted on a Microsoft Exchange Server? That is notorious for the behavior you mention here. Google for a variety of “home remedies.” When I get tired, I will Apple-U to mark it read manually. Sometimes I have to do that twice. What is particularly pernicious is if you have multiple inboxes and you get a copy of the email to more than one Inbox. The new and ‘improved’ Mail.app will mark the non-Exchange message read, but leave the Exchange message unread, and the UI does not let you know there are actually two messages unless you look into the individual Inbox.