[Toadling]

OmniFocus leaves them flagged because completing an action or project doesn't necessarily mean that it should be unflagged. In fact, I like to leave mine flagged so I can easily pull out those special items later.

I think what you probably want is to setup your "Flagged" perspective to show only remaining or available items (3rd menu from the left in the view bar, 4th if you count the project menu).

Does that help?