When you assign a new WF to a scope, the pages will not show up in the WF automatically unless someone start to work on them. But there is a way to double check if the WF was assigned correctly. Go to one of those pages, go to Properties > Workflow and see if the WF you assign is been set there. If so, it's correctly been assigned. The page is sitting at the previous stage which was published before the WF was assigned.