Mountain Lion Mail - Can't see time machine recovered mailboxes

If anyone can please help!

Somehow upgrading to mountain lion I lost mail. I recovered these from time-machine. For a while I could see them in the left-most pane under a heading called Time Machine. But in archiving some old content this folder-header (like iCloud or on your mac) disappeared. I know that the mail is still there as I can search for it. Weirder still, if I create a new mail-box I can see a Time Machine folder under 'on your mac'. I just can't get to the mail! The screen-shot below shows two folders (one containing all my recovered mail sub-folders) in the 'create a new mailbox drop-down' but only one in the left-pane under 'on my mac'.

I really need to be able to use this mail; sort of why I backed it up....