How do you mean "3 mailboxes"?
Three mailboxes on one address (the Inbox and two other folders)? Migration should have moved all mailboxes.
Three separate accounts (each with its own Inbox), perhaps as part of a MobileMe Family account? Each would have to be migrated separately.
Three incoming addresses (a main address with two mail aliases)? The aliases should have been migrated with the main address, but there are reports of some being left behind.
Unfortunately, you did need to migrate each portion of a family pack separately.
You should still be able to migrate the other two. Visit me.com/move and see if it offers you the chance to move an account to iCloud. I don't have any remaining family accounts to test it, but the residual MobileMe help system says migration should still work for a while.