Mail going to junk folder is not marked as junk

I have an automated email that I get occasionally. Without exception it ends up in the junk folder. However, even sitting in the junk folder, the message itself is not marked as junk.
I've turned off all rules, and they still go to the junk folder. Any ideas?
may be relevant: the email address is a google business apps email address.

There are quite a few threads discussing this.
Google is likely moving the items into it's spam folder which shows up as "Junk" in Mail.
Since Mail did not put them there, it doesn't mark them as Junk as it has no idea why they were put there.
As Gmail is IMAP-ish, your local copy matches what is on the server. Since it is in Spam on the server, it shows up in Junk in Mail.

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