Here is a message I have posted to the Apple support page:
Recently I have decided to simplify my email life and in doing so I have for one thing stopped my subscriptions to the hundreds of security and programming related mailing lists I once subbed. Doing this allowed me to get rid of the hundred or so folders I had called "FreeBSD security" and whatnot and I have created one folder called "Old Mail" and several sub folders called "2004", "2003" and so on. This has worked very well for me as I no longer need folders to keep things sorted out and I can Spotlight whatever I am looking for.
The mail I have placed into my "Old Mail" folder only shows up on the system that I have archived it on... When I go home I only see the archived mail from earlier that morning before I went to work and vice versa. I am using IMAP and I have verified that the email DOES EXIST on the server which is a good thing. I have tried the "Synchronize" function and it does nothing to solve my problem. I am not too worried as I know my email does at least exist on the server, but it is very annoying to only have access to half of my archived messages at any given time.
So what should I do?
I'll keep this page updated as to what happens.
UPDATE I had to take the link off of here because apple's stupid discussion board website isn't smart enough to convert "&" to the non-XHTML compliant & character which it needs to be able to do in order to allow people who care about being XHTML 1.0 Strict compliant (like me) to post a link to their board from a website.