Are you mysteriously missing new messages in Apple Mail? Apple Mail’s Smart Mailbox feature works great, except when it doesn’t. Several clients have had sudden mysterious Apple Mail problems, such as incoming mail going directly to Trash or losing a new message entirely.  Looking into the typical possible causes, such as spam or junk mail filters or another device stealing the message, or rebuilding the INBOX, proved fruitless. The mystery turned out to be a correctly configured Smart Mailbox that went suddenly rogue for no apparent reason which caused the missing email problem.  When the Smart Mailbox was deleted, missing mail was no longer an issue. I have no proof, but I think this issue is symptomatic of a corrupted mail preference file in the user Library/Preferences folder.