I just started having this problem every time I delete an email in Outlook.  I don't recall making any changes to the settings, so I'm not sure how to fix this.  Whenever I delete an email, it immediately sends the email to the trash just as it should.  However, a few moments later once the folder syncs, another copy of the same deleted email will show up and mark itself as unread.  Basically, I will end up with duplicate deleted emails and one of them is always marked as unread.