If you tell VPOP3's POP3 mail collector to leave messages on the ISP's server for a few days, you may find that sometimes VPOP3 will redownload all the messages from the ISP mailbox again.

VPOP3 (like other email clients) keeps track of which messages it has previously downloaded, by remembering their 'Unique IDs' (UIDs). This problem usually happens if VPOP3's remembered UIDs do not match the ISP's UIDs.

The POP3 standard mandates that the messages' unique IDs should never be changed. However, some ISPs will re-assign UIDs to the stored messages. Good ISPs will limit this to when there is an otherwise unrecoverable error in the mailbox store on their server, and will treat it as a major problem, issuing warnings of the consequences (i.e. duplicated messages) to their customers. However, many ISPs will do this without warning their customers, and a few seem to do is as a 'preventative' measure, monthly, or even daily.

If the ISP does this regularly, then you should contact them and ask them to stop doing it…

With recent versions of VPOP3 you can tell if this has happened by looking at the 'Received' headers of the message. The line which the VPOP3 POP3 collector adds shows the UID in the header line (UIDL=….), and you can compare the downloaded copies of a particular message. If the UIDs are different for the same message, then the ISP has re-assigned the messages' UIDs, so VPOP3 sees all the messages as ones it has not seen before