Various E Mail problems: Junk Mail, Log Off, etc

Question

I am having various and frustrating problems that are intermittant.
I have two incoming e mail accounts, one is IMAP and one is POP.
1. Junk Mail. After having reset my junk mail settings as advised on this site just a few days ago, I am continuing to experience this problem. Messages that the systems "knows" is Junk Mail do NOT go to Junk Mail folder, but to the regular In box. It knows they are Junk Mail because the Tab for changing the message at top of screen says "Not Junk", which means it thinks it is JUNK. They why won't it go into Junk Mail folder?
2. When I try to delete these messages one by one in In box, the computer "freezes" and takes forever to delete the messages. The In box counter on left hand side of the screen does not decrease as I delete messages, but takes a long time (minutes) to catch up with the deletions.
3. When receiving certain e mail from specific recipients, the system intermittantly says "message not dowloaded from server, you need to take this account on line". Well. it IS online! Again, this does not happen all the time, but often enough and from the same e mail recipients) that it is very frustrating.
4. Oftentimes when I try to shut down, I get the dreaded spinning color wheel, only to have to force quit. This is a lengthy process, and then I lose all of the deletions that I have tried to make to my Inbox.
Are all of these problems somehow related? Cumulatively, they are very frustrating. I never had these kinds of issues with Windows Mail apps. Uuughh!
Thanks for reading and any assistance.

Answer 1

There appears to be a problem with the index.
Verify/repair the startup disk (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all the filesystem issues, if any, and ensuring that there’s enough space available on the startup disk (a few GB, plus the space needed to make a backup copy of the Mail folder), try this:
1. Quit Mail if it’s running.
2. In the Finder, go to ~/Library/Mail/. Make a backup copy of this folder, just in case something goes wrong, e.g. by dragging it to the Desktop while holding the Option (Alt) key down. This is where all your mail is locally stored.
3. Locate Envelope Index and move it to the Trash. If you see any other “Envelope Index”-named file there, delete it as well.
4. Move the “IMAP-” account folder to the Trash. Note that you can do this with IMAP-type accounts because they store mail on the server and Mail can easily re-create them. DON’T trash any “POP-” account folders, as that would cause all mail stored there to be lost.
5. Open Mail. It will tell you that your mail needs to be “imported”. Click Continue and Mail will proceed to re-create Envelope Index — Mail says it’s “importing”, but it just re-creates the index if the mailboxes are already in Mail 2.x format.
6. As a side effect of having removed the IMAP account folder, that accounts may be in an “offline” state now. Do Mailbox > Go Online to bring it back online.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. That is, ~/Library is the Library folder within the user’s home folder, i.e. /Users/username/Library.
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If the problem persists, what are your Preferences > Accounts > Mailbox Behaviors > Junk settings, particularly for the IMAP account?
Also, what have you done to “reset [your] junk mail settings as advised on this site”? This is what I’d suggest:
1. Go to Preferences > Junk Mail, disable junk mail filtering, then enable it again. This resets the rule that governs what the junk filter does.
2. Choose either Training or Automatic mode (it doesn’t matter) and leave the other options checked. Click Advanced to see how the junk filter rule is defined now if you want, but don’t touch anything there.
3. Reset the junk filter database (Preferences > Junk Mail > Reset).
4. Open Window > Previous Recipients and get rid of any addresses that you don’t want Mail to treat as legit.