Where does Outlook 2007 keep a mark of emails downloaded using POP3 protocol?
I believe it would be stored in the PST file, or the information required is at least contained in there. I had a look through the [MS-PST] specification but I couldn't see anything in particular that indicated where the flag was stored.
It may be an algorithm that determines whether the mail has already been received. For example, if the mail engine enumerates mail on the server where it looks at the sender, recipient, timestamp and the account that the mail is being received on then it will not download the email.
I believe this is plausible, as when you recreate your mail profile and specify the same PST file in certain situations mail will be downloaded again. This is because the account that you are downloading the mail from is different (a different GUID/ID that Outlook uses to track the accounts internally).