Mail.app draft not removed and displayed in thread

In Mail.app on 10.10.1, when I compose a draft it is displayed inline in the conversation thread as soon as it is auto-saved or I manually save the changes as I am typing. So it's actually rendering the text twice - once in the "Compose" window and once in the mail messages window. This seems really odd to me.
Furthermore, as soon as a draft is saved, it never leaves the Drafts folder, and must be manually deleted. It does not matter if I send the email or cancel the message - it's stuck. I do not have "Store Drafts on Server" checked for any of my IMAP accounts, and the Drafts for my iOS devices are all set to store drafts on the device.
The constant stream of stuck draft messages is infuriating enough, but to see them inline in conversations is downright weird.
The issue does not effect iOS devices, and works fine on Mountain Lion; it's just Yosemite's Mail.
I have repaired permissions, and set and unset the settings, checked and double checked setting - all to no avail. Any suggestions?

Linc, you are so helpful to this community it's just astonishing. Thanks for all you do.
The rebuild was a great idea, but did not solve the issue. I narrowed it down to the GPGMail bundle, which I thought I had disabled when I was testing, but I clearly erred. It seems like a known issue, and the excellent team working on that software is, I am sure, on top of it.
Again, thanks Linc!

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