If you're donwloading vai POP3 to Outlook and you still have copies on the sever that are being marked as read I assume you're "leaving a copy of the messages on the server" for a determined amount of time? If this is the case you can expect some intermittent duplication problems with email. All of a sudden you'll get mails that you got weeks ago, all over again. Hasn't happened as much lately but it used to quite a bit, still don't understand what causes it after talking to support but have just taken to living with it when it happens, kinda like spam.
If you're accessing your mail to download it, it's basically like reading it, so no, there's no way I know of to leave it marked as unread if it's been accessed by Outlook.