macosmail.appspam
Here is the Junk Mail settings:
Also, junk mails are shown in Smart folders even when the "Message is not in mailbox Junk" condition is set ("Contains messages that match" is set to "all" as well).
Messages are identified as junk by Mail.app (they color is yellow and the icon is shown).
My question is how to make Mail app to hide junk mails in all non-Junk mailboxes.
For some reason or another, Apple has made it impossible to access junk messages from a Smart Mailbox.
If you are able to set Message is in Mailbox to Junk, you must be setting it to a special 'Junk' mailbox that you have created (or that was created automatically by whatever email service you connect to). So, messages in Mail's built-in Junk folder won't appear in your mailbox.
However, you can get around this without too much trouble. To do this, make a Mail rule that automatically moves junk mail to your special Junk mailbox. Here's how:
Go to Mail-> Preferences-> Rules. Click Add Rule. Set the description to something like Move to special Junk. Set the popup in the first box to Message is Junk Mail. Set the first popup in the second box to Move message, and use the second popup to select your special junk box.
Now, any incoming messages that Mail thinks are junk will go to your special junk mailbox. You can use this one in a Smart Mailbox.
Hope this helps!
Update - Mail has a filter option to the right of the 'sort by' at the top of the email column where you can choose which mailboxes, or to only show unread, etc.
Best Answer
Is it an IMAP mailbox? I had this problem with my self-hosted IMAP account, where iMail couldn't move the message into the junkbox on the server and kept finding it in the inbox. I deleted the IMAP account, it's associated mailboxes on the server and started again and it worked alright.