What kind of email account is it? Do you have access to it from another location/device as well? One thought that comes to mind is that the email account is capable of being accessed as a POP3 account and an IMAP or Webmail account. When being accessed as IMAP or webmail, the email stays in its location 'in the cloud', but when being pulled by a POP3, it is copied from the server to the local device and deleted from the server (at least many times is the default setting for POP3 email handling).
Then again, maybe its ALL spam, so Outlook shuffles it to a spam folder, or you have some sort of rule set up so that the email moves to another folder. No idea.