Apple Mail doesn't apply rules unless I choose "Apply Rules" manually

I found following post: http://www.cnet.com/how-to/how-to-delete-and-manage-old-messages-in-os-x-mail/

So you have to do the following:

1. Add your filter that you want to apply.
2. Add the rule condition: Every message.
3. Set the drop down to "all"

You need to set "all" because if you set "any". What happens is that it evaluates every message, it will automatically match "every message". Then because you set "any". It won't consider the actual filter. Then it'll execute the action. So if you set the "delete" action. You will automatically delete every message in your inbox. A very dangerous mistake.

This is a bug.

In their infinite wisdom, Mail.app developers decided only to apply rules to 'unseen' messages. If the IMAP 'seen' flag is set, rules will not be applied.

I started a forum thread on the apple forums on this topic.

I had the same issue, but it turned out the first rule in the list (News from Apple) had "Stop evaluating rules" as the last action.

I removed this action and it worked fine.

Not sure if this is exactly your problem, but something similar happens to me.

I've got a Mac running Apple Mail and an iPod touch, both checking the same IMAP account. The Mac is asleep during the day. While out and about, I'll check my mail on the iPod, read the new messages, and leave them in my inbox. When I come home, I wake up the Mac, and Mail syncs with the server. The filtering rules are not applied.

The reason for this behaviour is that Mail only appears to apply rules to "new" mail. Having already seen these new messages on another device, I'm not so much downloading new messages to Mail as I am synching with the server. So, no rules applied for these messages.