If you have a comma in your long username, then it appears it can cause those problems in Mail.app where it states "the mailbox ... is already in use by ...'. This happened to me when when I had my long username as "Lastname, Firstname."
It seems that sometimes the system had opened files as user "Lastname," not as my short username or full name. When I took out the comma in my full username, all my problems went away. I am surprised that the OS lets you put a character in your username that causes this problem! I'm not sure if this happens with other characters too? Now those stupid errors when checking or quitting Mail are gone!
Mac OS X Hints
http://hints.macworld.com/article.php?story=20020915053619379