Hey @DougHarrison, it sounds like your settings may be a bit off. Typically if you chose and option like "Leave messages on server" or maybe a "Leave messages on server, mark as read"... If you have multiple devices accessing the same email address there is a period of time where your iPhone and iPad may both have a message as unread. Additionally when you read a message on your iPad the notification may remain on your other device until the next refresh or check of your emails.
I'd just double check your settings but sometimes it is just a matter of waiting for the message to be marked read on your email server AND other devices to update to the new status. I hope that helps?
roy darling *my posts seem a lot shorter in my head