I originally posted this about a year ago, and the problem still persists in Mail on OS X. So if you have problems sending mail that’s been filtered into folders, this explains why; you’ll need to check each message before sending to make sure it’s using the correct outgoing email address.
I’m on a few email mailing lists, and I’ve noticed that Mail, in OS X 10.8, has been doing something odd. Generally, if you have multiple e-mail accounts, when you reply to a message, your reply uses the same account the message was sent to. But I’ve been finding that Mail does not correctly choose the account if messages are filtered into folders; messages bounce because the selected account is not a member of the mailing lists.
There is a setting in Mail’s Composing preferences where you choose which account to use for new messages, but this shouldn’t affect replies.
The problem only occurs when mail is filtered into folders, which I do for mailing lists. If messages are in one of my inboxes, replies use the correct email address, the one that the message was sent to. But if not, they use the default address which is set in the Composing preferences, as shown above.
So, if you filter emails into folders, and have multiple accounts, you need to check every single e-mail you send as a reply from any of those messages. You can do this by looking at the From popup menu when you’re sending or replying to an e-mail. But this is a very serious annoyance, and I hope this gets fixed.