MacFixIt reader Ben Summers reports an issue where Mail will not download messages that do not contain body text:
"I reported this to Apple ages ago, but they're still ignoring the bug report, and haven't fixed it...If a message stored on a POP3 server has no content, Mail.app will fail to download and delete it. If you're quick enough, you can see x/y messages in the status bar, but otherwise there's no UI indication of the problem. I missed an important, but zero length, message with all the content in the subject.
"Steps to reproduce: (1) Send an empty, plain text, message to a POP3 server; (2) Attempt to download it.
"The result: (1) The UI does not acknowledge the existence of the message; (2) The message is left on the server; (3) A line like this is found in console log:
2004-03-26 16:08:03.654 Mail failed to append message [POPMessage: 0x56a0f50] (_rangeOfBytes: Out of bounds)
"This happens reliably with all 0 length messages. Bizarrely, about 8 or so spam messages a week look like this (of the 2000/week I receive)."