With most POP 3 accounts (severs) an e-mail client downloads the mail from the sever and thus it is then deleted from the sever. The feature in plus! asks the sever and the sever reports the total number of e-mails on it but since the previous messages were downloaded they were deleted after the download. Then when new mail comes it counts that. Thus I don't think there is
any way around it.
Sorry it's not clear
and feel free to correct me if I'm wrong.