If you use Mail 2.0 with an IMAP server, and you changed the "IMAP Path Prefix" after having received mail for a while, you should check the contents of the IMAP-yourAddress folder in ~/Library/Mail.
The way Mail aggressively caches things means that there are probably old caches in here of public folders you no longer see, so you can safely delete them. The way I handled this was to delete everything inside the folder (~/Library -> Mail -> IMAP-yourAddressHere) and just let Mail regenerate the caches. Make a backup before you do so you don't lose any data, but it seems like it's worth a shot.
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