I’ve tried everything I know and searched everywhere, but I can’t find an answer to this problem. Several of my clients have this issue and now I have it, after adding two new accounts to Mail – both of the new accounts are effected, but the older ones work fine.

Mail picks up email and filters out spam just fine. The problem is with emails I have either deleted or flagged as spam. Mail doesn’t remove them from the server even though I have my preferences set to delete them “Right Away”

Then the next time Mail pickup email, it picks those same messages up as “unread.” No matter how many times I delete them, they keep coming back as “unread” messages. If I manually delete them, using the “Remove Now” button in preferences, that solves the problem.

I have repeatedly rebuilt these mailboxes since creating the accounts a few weeks ago, but I keep having the same problem. The server recognizes them as “read” becasue I can delete them manually, but apparently Mail thinks they are unread.

If Mail.app starts behaving weirdly, you could try deleting all the preference files and starting from scratch … note that doing this will delete all e-mail account settings, so it’s a good idea to write down all the relevant details first:

WARNING: This is the “so-called” Nuclear Option, for reseting your mail, keep reading first…

• Quit out of Mail.app
• Backup up your mail & preferences
  • Backup com.apple.mail.* from your Library/Preferences folder
  • Backup ~/Library/Mail
• Delete the com.apple.mail.plist file (it’s in your user accounts’ Library/Preferences folder)
• Delete the MessageUidsAlreadyDownloaded file (it will be in your user accounts’ Library/Mail/POP-user@mail.internode.on.netfolder)
• Open Mail.app and run through the setup wizard again
• Import all of the mailboxes back in to Mail.app

It’s a relatively complex procedure, but it’s helped me out once or twice when everything’s gone haywire.

The above process is fairly radical and effectively forces you to recreate your mail setup, if it’s a minor issue, it maybe better to address the issue directly.

Try, Quiting Mail, and just deleting your MessageUidsAlreadyDownloaded file, but make sure that you have a complete backup.  There have been reports that it resolves the issue easily, and simply.