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I have the same problem as the original post. Have tried resetting the filter but so far its just a terrible mess. The junk mail filter worked great until the MacOS 10.1.xx update and then - disaster. Is there a file somewhere that holds the junk/not junk info that is missing or has the wrong attributes?
 
Did you also go into the Gmail Spam folder, check the message, and click 'Not Spam?' Apologies if you already did/have done this step before.

Actually, gmail is not the problem. It's irrelevant what the client side is doing. The point here is that Mac's Mail app is marking stuff that it thinks is Junk, irrespective of what any clients are doing. And then not learning what isn't junk when you mark it as such.
[doublepost=1481647687][/doublepost]
I have the same problem as the original post. Have tried resetting the filter but so far its just a terrible mess. The junk mail filter worked great until the MacOS 10.1.xx update and then - disaster. Is there a file somewhere that holds the junk/not junk info that is missing or has the wrong attributes?

Sorry to hear that you're suffering similarly, too. Have you told Apple?
 
It looks to me like this is fixed by installing the Sierra 10.12.2 release that just came out. After I installed that release I reset the junk filter and it's been working properly and learning since then.
 
The 10.12.2 update (which updates Mail to 10.2) looks very promising. Mail seems now to be consistently learning what I mark as Junk or Not Junk. Fingers crossed it remains that way.
 
Although you're talking specifically about Junk I have experienced similar problems with the 'Move to' folder option. It just wasn't reliably making predictions, even with seemingly identical emails in the important fields like the sender. I assume the intelligence behind the move prediction and junk are similar.

Just like you my initial impressions of 10.12.2 are that it has improved markedly.
 
As I said in post #11, you have to add it by using Customize Toolbar - right-click anywhere in the toolbar and you'll see "Customize Toolbar" at the bottom of the popup. Choose that, and then drag to your toolbar what you want from the "Drag your favourite items to the toolbar ...." section that appears. In this case the Junk icon. Then when you highlight a message the app has decided is junk, the Junk icon will turn into a Not Junk icon, which you can click if you disagree. However ...

This is a sidetrack. My main point in starting this thread was that, even if you get the Junk/Not Junk icon, and even if you start marking stuff the app says is junk as not junk, the post-Sierra Mail app is not learning this as it should, and as it always has done prior to Sierra.


IT IS NO LONGER A BUTON IN THE TOOLBAR FOR "NOT JUNK" - YOU CANNOT ADD THE BUTTON
 
IT IS NO LONGER A BUTON IN THE TOOLBAR FOR "NOT JUNK" - YOU CANNOT ADD THE BUTTON
There is no "Not Junk" button BUT if you go to the mail that is marked as Junk and use the "Move to Inbox" option, it will move it to the corresponding inbox and mark it as NOT JUNK at the same time.
Screen Shot 2017-03-10 at 18.40.00.jpg
 
There is no "Not Junk" button BUT if you go to the mail that is marked as Junk and use the "Move to Inbox" option, it will move it to the corresponding inbox and mark it as NOT JUNK at the same time.View attachment 691748


Awesome - thank you, useful. I didn't know if moving to the inbox would keep the same messages from ending up in junk again.

Something else I just noticed, the JUNK button changes, and it is almost impossible to see, from an UP arrow (not junk) and a DOWN button (junk) depending on the situation. Very difficult to see.
[doublepost=1489161399][/doublepost]Very refreshing to post a question or comment and not get attacked by somebody who is a Level 50000 specialist who has no clue what your asking, has never had the issue, refers your to a completely unrelated and outdated help article and then says if that doesn't work, you should reinstall your operating system :)
 
Awesome - thank you, useful. I didn't know if moving to the inbox would keep the same messages from ending up in junk again.

Something else I just noticed, the JUNK button changes, and it is almost impossible to see, from an UP arrow (not junk) and a DOWN button (junk) depending on the situation. Very difficult to see.
[doublepost=1489161399][/doublepost]Very refreshing to post a question or comment and not get attacked by somebody who is a Level 50000 specialist who has no clue what your asking, has never had the issue, refers your to a completely unrelated and outdated help article and then says if that doesn't work, you should reinstall your operating system :)
Aaah, those level 50000 "specialists". I'm actually surprised when and if they do offer something useful. ;)
 
Aaah, those level 50000 "specialists". I'm actually surprised when and if they do offer something useful. ;)
I know this is an old thread, but the absurdity of how Mail deals with marking mail as not junk (meaning it does not work at all) is even more absurd when you consider that mail to me from APPLE (receipts for purchases) is marked as junk, and future mail stays junk even when Not Junk is clicked. How can Apple's own mail system fail to recognize mail from Apple itself as legitimate? How can Apple's own mail system fail to allow whitelisting mail from Apple itself? Isn't anybody paying any attention there?
 
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