>> then go back to marked as unread when it next updates
I understand that when you see the message change in Outlook, but..
...does the change on the mail server (web mail) happen right then, or at some earlier point? You should be able to tell by having web mail open at the same time.
As for Aqua, do you use IMAP push in this account / folder? Can you try turning it off to see if it makes a difference?
And as usual, the only way for me to really investigate, rather than to throw out wild guesses, is if you captured the issue in the app's debug log (see just below).