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Here is the Junk Mail settings:enter image description here

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.

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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.

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Yes, it's google's IMAP. The full reset is the last thing I want to try, though –  Kentzo Dec 27 '11 at 17:54
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Try going to mailbox behaviours and disabling "Store Junk Mail on the server" edit- I think this will only affect future junk, though. –  George Pearce Dec 27 '11 at 18:12
    
I'll try and post the result. But did you mean it's expected behavior? –  Kentzo Dec 28 '11 at 15:37
    
Not sure I fully follow - but I think the reason is that the closest thing to a folder on GMail is a label, which doesn't require the message to leave the inbox. So it gains the label 'spam' on the GMail interface, but doesn't actually leave the inbox folder - and therefore the filters. By storing the spam folder locally, iMail will remove the post from the inbox entirely and put it into it's own local folder. I can't promise that's right but that's how I understand it :-) –  George Pearce Dec 28 '11 at 15:54
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