Yeah. It could be that both PC are set to leave the messages on the Server. So that when she downloads them at home they are still technically new. Since they were not read or removed from the Server.
Tell her to make sure her Email at home is closed out so that it doesnt downlaod to both places. Could be that she gets it at her home email application first then gets it at her work on. Also make sure it is not setup to leave the mail on the server. If she must have all her mail at both places then she will have to continue to do what she is. Since no matter what the mail will technically be new at each place.
The only other option is that she manually goes on to the mail server and marks them as read at work then when she gets howm they are not downloaded.