What Is Putting Mail Messages In Junk Folder?

The Junk folder is there, but empty. There is still the elusive settings where you can’t set any mail rules.
 
Whoa! I was planning to update to 10.11.4 this morning until I saw Cheryl's note. Was the security "fix" part of that?
 
I have not changed over to 10.11, so the security update was for 10.9. It could very well be a similar security issue for all versions. I do have an update on my ‘issues’

Junk folder on iCloud web is still working but it must be some rules that are hidden from the user. I found emails on the web side that should not have gone to Junk and I had to move them.

I got home from work and started up mail...to my dismay I got the warning that there was something wrong with my @mac account and I should open iCloud preferences to fix it. Opening iCloud preferences brings me to the account preference pane. Nothing wrong there. Went back to Mail and I got that warning again. This time I opened Mail preferences, nothing wrong there. Then it started working.

Do I upgrade to El Capitan? I had been avoiding it because to the trouble some people had. Work took over and I haven’t been up to speed on how it is now.
 
More on that junk folder:
Since my 4+ hours in trying to straighten out my iCloud problem I found the reason to getting those warning windows that there is a problem with my iCloud account. I had changed the password to my AppleID many moons ago. Apple now uses the Apple ID to connect to iCloud (which includes email). I had to go into Keychain Access and hunt down all the ‘keys’ saved for AppleID and iCloud, deleting the super old keys and updating the most recent ones with the updated password. Now I no longer get that message and Mail is behaving properly.

Junk Folder - As stated earlier the separate listing of the Junk Folder under iCloud is gone, but iCloud has not stopped deciding what is Junk. When I get mail through Mail app, what Apple thinks is junk now goes to Mail’s Junk folder but it is not labeled as junk like Mail does to the ‘real’ spam. These are the same emails that iCloud indicates as Junk on the web site.

What’s funny is that iCloud thinks the emails from iTunes and Apple are junk. o_O
 
What’s funny is that iCloud thinks the emails from iTunes and Apple are junk. o_O

Last week I bought an item online from the Apple Store. All related emails were plopped into the Junk folder - order, shipping, ... As I think I said before, I just treat this as another "inbox" - a manual fix until Apple supplies an automatic fix.
 
Hello, again! This problem has gotten much worse for me since around the start of this year. On top of making really bad decisions on what's junk, ...
  1. Some incoming messages simply vanish. They don't go to Junk or to Trash, just ... nowhere ... but not immediately. I have watched a message dematerialize right before my eyes. It was like watching an old Star Trek episode. (Beam me up, Scottie!)
  2. At least one received message has become persistent. That is, if I trash it and then empty the trash, the message will reappear in my inbox later - minutes, hours, days. The body appears to be corrupted - most of it looks OK, but there's gibberish at the end. The message is from my sister who is not usually prone to gibberish.
Item (1) made me suspect SpamSeive, so I turned it off for a while. Same behavior.

I created a new email account at a non-iCloud server and then directed my iCloud account to forward everything to it. The forwarding works, but it happens after the junk decisions. So I restored things to normal.

So, after all these months, does anyone have suggestions?
 
Do you have SpamSieve updated to the latest version?

In Mail preferences>Junk Mail There is a line at the very bottom of the window: "Filter Junk Mail before apply my rules” - uncheck that box if you have it checked.

Do you have another device that is actively getting Mail as well? I wonder if it is causing the disappearing act?
 
I have disabled Mail preferences>Junk Mail ever since I installed SpamSeive, and, yes, I have the latest version. I looked through its blacklist but found nothing even close to my own domains or accounts.

I use Mail on my iPad, but there are no rules or filters there. That said, I have also seen the vanishing act there.

Speaking of SpamSeive, I found directions from them on how to perform a complete rebuild of the Mail database. Since Mail's own rebuild menu item did nothing, I did the complete one. That has fixed the corrupted messages and their looping appearances.

So, some progress ...
 
I may have stumbled onto a partial solution. It was triggered by an unrelated event where I purchased an item online. On the final step after SUBMIT, the page advised me to look in my spam folder in case I didn't see the email receipt right away and, to prevent future such mishandling, add their address to my contacts.

Hmmm. I logged into iCloud and looked in my Junk. Sure enough, there were the usual suspects: bank, broker, ... So for each one, I added the FROM address to contacts and clicked NOT JUNK. That was around two weeks ago and ... no repeats so far!

If anyone else has this problem, please try this trick and report back.
 
Just my two cents...

Based on the complexity of iCloud Mail (via browser) vs MacOS Mail vs iOS Mail AND given that it seems clear that it's Apple's iCloud servers that are predicting which email messages are considered JUNK, I think the responsibility lies with Apple to provide more robust rules that can be set, for example, within iCloud Mail that will be then applied regardless of which device is used to access email.

This doesn't necessarily have to be extremely complex; it could be as simple as allowing a new rule like:
IF SENDER does not contain @apple.com
- OR
IF SENDER does not equal news@apple.com
that could be added to the other pre-built rules.
 
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