I was having some problems with Mail.app and it's handling of cached IMAP folders. When I would delete all of the messages in a folder, then when I tried to view new messages it would still display old messages that I had deleted from the server. The issue seemed to be that the folders were missing the "special" message that is in all IMAP folders. I had been using mutt and procmail for quite some time before I switched to IMAP, hence none of my folders had the special message that helps keep IMAP clients on the straight and narrow. So if you are seeing odd caching bugs, try deleting the folder and re-creating it through the Mail.app interface, especially if they were just procmail mbox files.