Mailbox Duplication? Gmail

I just added a new Gmail email address/account to Mail (4.5). It shows up twice in the Mailbox Column...once under Mailboxes at the top and once at the bottom of the page under its own name. Some of the mail that appears in the 'All Mail' folder in that bottom mailbox does not show up in the mailbox at the top (or show up as new mail in the main window). How do I eliminate the bottom one?