Mail folder structure: where are most recent messages?
If Mail stumbles across a specific messages when accessing the mail server via POP or IMAP it might help to remove the offending message directly on the server. The easiest approach in this case is to access the mailbox via webmail (at least if your provider offers this). Alternatively installing another mail client (e.g. Thunderbird) and using it to delete the offending mail might help as well.