I asked this question on serverfault, but it was correctly suggested that superuser is better -- and I agree:

My wife and I share a Mac and use different accounts. We both use Apple's standard Mail.app. We can also get to our email accounts via SquirrelMail that our webhost provides. Both SquirrelMail and Mail.app are connecting via IMAP.

My wife was the first to notice that not all messages were getting to the Mail.app. She would check the Mac (our main machine) and then a little while later check mail from another machine via SquirrelMail and see messages there that should have been on the Mac. She would go back and those messages would never show up.

Lately, I have been seeing the same thing, though less often. I can't reproduce it, or just look at a message to see if they haven't been moved over. I've looked in Junk, etc. and the Mac simply never sees those messages via IMAP.

Does anyone have a guess to something I could poke around at?