There are times when his POP3 email didn't show up in Outlook and he'd have to restart in order to see it. We've changed various Outlook/Internet email settings, the Outlook Send/Receive settings, and have updated Outlook 2003 to 2007 but cannot resolve the issue.
If that's not the case, I would create a new MAPI profile on a new computer with the user's settings. If that works, the culprit was something environmental on the user's original computer. From there, I would try creating a new MAPI profile on that computer to see if it resolves the issue.
If creating a new MAPI profile on a new computer doesn't resolve the issue, then you'll need to check with your ISP, or see if there is something strange happening on your network at the times in question.
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