I've been having this problem for several months. In fact, I was experiencing it on my G5 tower, under 10.5.6, and I had hoped that replacing the entire computer with a new iMac, and a brand new operating system, would make it go away. No Joy. Apparently the MIgration Assistant helped the problem migrate to my new machine.
But I'm posting this because I think it's significant that the problem exists independently of the operating system or hardware. I think there is some kind of plug-in or extension which can be transferred between machines and software versions.
Specifics: I can't quit mail normally on the desktop which was migrated from my old machine. 'Quit' grays out in the menu, but the program doesn't stop running. I can compose, send, and retrieve email as if nothing is wrong. This problem does not appear when I create a new desktop account and log in on that one. Mail quits normally on that desktop. But on the migrated desktop, I can never quit normally. Force quit will work, though, which is an improvement over 10.5.6, when I had to do a hardware reset.