Mail freezes on quit (sort of)

Apple Mail (6.3) in Mountain Lion (10.8.3) won't quit.
Weirdly, the message I have selected when I try to quit stays in the main window. Also weirdly, I can click around to different messages and pull them up in new windows...while the main window stays locked into the same message.
When I bring up the force quit window it doesn't read that Mail is not responding. But it won't let me quit out with command-Q.
Even cancels shut down.
I can force-quit but that's annoying.
Any ideas?
Thank you,
Stef

Have you tried to rebuild the mailbox? To do it, open the Mail app, and then, go to Mailbox menu (on the menu bar) > Rebuild

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