Mail.app stores meta information in its Envelope Index, a sqlite database. Sometimes this database gets corrupted and you’ll have weird things like duplicated messages (that aren’t really duplicated) or messages that appear not to have senders or subjects (even though they do). If this happens to you, quit Mail, look in ~/Library/Mail for the file named “Envelope Index”, move it to the Desktop or the Trash, then launch Mail again. You’ll get a dialog asking if you want to import now or later, and you should click the button for now.
Then wait.
Side note: I’m almost at 100K total messages stored. I wonder how many I get per day now.
