Fixing Smart Mailboxes
I'm going to assume you are using Mail 8.2.

Have you checked the permissions on the SmartMailBoxesLocalProperties.plist in ~/Library/Mail/V2/MailData? For reference my plist -rw-r--r@.

When you state new smart mailboxes are working, does this mean they aren't being saved also? The fact that new mailboxes aren't working either seems to point to a permissions problem, as seen in this previous question.