SpamSieve 3 brought a new way of integrating with Apple Mail—using a Mail extension—that’s compatible with macOS 14 Sonoma and later. Most customers have had success with this simpler system, where there’s no plug-in to install or rule to set up. Unfortunately, some customers have encountered a macOS bug where Apple Mail stops sending new messages to SpamSieve’s Mail extension. This causes spam messages to be left in the inbox, not because SpamSieve thought they were good, but because it hasn’t actually seen them.
The Check inboxes for new messages not sent to Mail extension option is a workaround for this bug. It automatically filters all of your inboxes, without your having to configure anything. Just make sure that option is checked in the Settings ‣ Apple Mail ‣ Setup window and make sure that SpamSieve has Full Disk Access. (Without Full Disk Access, the feature will still work, but it will be slower and report an error for mailboxes containing more than 5,000 messages.)
Inboxes are periodically checked for new messages according to the same schedule as Filter spam messages in other mailboxes. Thus, there can be a slight delay before SpamSieve detect new messages. You can optionally enable the Add green flag to unread good messages option if you want to see whether a message in the inbox has in fact been processed.
See also: Why are Apple Mail inbox messages not being processed?.