It's true that if you move messages to a gmail or other webmail account, this problem occurs. I think, though, that the many messages emphasizing that usage may have confused the issue for some posters to this thread. It's only one of several use cases where this problem manifests.
I agree with Paul Mycroft two posts up. Messages that are moved out of their original inbox -- either manually or by email rules, for whatever reason -- lose their account identity when you reply to them. Instead of replying from the account to which they were sent, they identify themselves as being from the topmost account entry under the "Mailboxes" header on the gray "Mailbox list" (there may be some variations in different use cases). Messages that are not moved reply just fine. It would seem that Apple has removed the element that identifies the receiving account out of the message and given that job to the default account, which isn't established by the Preferences setting (Preferences ... Composing) that's supposed to handle that job, but is instead controlled by the order of the account inboxes in the folder tree.
Even an iOS 6 Mail message remembers its received account when you move it and reply from the new location.
It's a bug, not a feature. Really, two bugs.
FWIW, my use case: My company archives all Exchange-based email after 30 days. By setting up an email rule to move all my Exchange mail to a folder "On My Mac," I'm able to search and review email months later. As a result, I have the problem. I've also encountered a related problem I haven't seen noted elsewhere: In some instances Apple Mail CCs my default account on some of my outgoing messages (and no, I don't have Automatically CC myself Preference setting checked).
The problem has been so productivity-robbing for me that I was compelled to switch to Outlook. But I'll switch back to Apple Mail when (if?) Apple fixes this.