Apple Mail moving to Archive

Hi all, I installed SpamSieve yesterday and I’m happy with it so far, however I have noticed for some reason since installation, lots of emails are moved straight to the “Archive” folder rather than their respective inboxes (both good and spam messages). I don’t want this to happen. Can anyone shed any light on this?

OSX Yosemite using Apple Mail.

Thanks

Installing SpamSieve shouldn’t change anything with respect to the archive. Are you sure that the Archive mailbox really is the archive? Sometimes Mail gets misconfigured such that it thinks that a regular mailbox is the special Archive mailbox. Then you may have a rule in Mail or on the server to move messages to that mailbox, and it looks like they are going to the archive. You can choose which mailbox the archive is using Mailbox > Use This Mailbox As > Archive Mailbox.