Phantom messages in Mail

I have two similar problems in Mail within Mavericks - essential a message count (of unread messages) is showing in the side bar when there aren't any in practice. This is currently happening for the following:

1. the 'Flagged' folder under 'Mailboxes' in the side bar. This shows 22 flagged messages - one red and 21 green. The green count is sort of correct (it shows that they are unread when in reality they have all been read and show as read when I click on the folder). However, when I click on the red flag folder, it says 1 unread when in reality there are no messages in that folder (either read or unread).

I've searched in Mail - status: Message is Flagged and it only brings up the green flags.

Any idea how I might get rid of this rouge label of 1 unread message? If I can also get rid of the 21 'unread' green flags that'd be a bonus too.

2. I have a smart mailbox which has the criterion to show unread emails (as emails generally go directly into their respective folders so this way I can see unread emails all in one place). Currently, this shows 4 in the sidebar. However, I have no unread emails (either in this smart mailbox or in any other mailbox in Mail).

I've tried rebuilding various mailboxes, I've restarted Mail and the computer. I've removed messages from the server.

Any thoughts?

Edward