If the log says that SpamSieve predicted it to be good, then the only thing SpamSieve would have done is moved it from InboxSpamSieve to Inbox (if you’re using the large inboxes setup). I wouldn’t expect that to cause the message to be archived, but it could happen if your rule is set to use an InboxSpamSieve folder in a different account.
If you don’t have a lot of messages in your inbox, you could try the regular setup instead.