You've already asked this question and received a few replies:
Missing mails on Macbook pro - please help
No need to start a completely new thread asking the same thing.
Specifically, look at my reply in that linked thread above. If you have set up a POP3 account on one machine, and have it set up to not leave messages on the server, then the messages will only be downloaded to ONE machine, not both. For them to appear on ALL machines, you'll either need to switch from a POP3 to an IMAP account, or modify your email client's POP3 settings to leave messages on the server when they're downloaded.