I’ve noticed this for a while now, only on the android app, not the web site. As an example yesterday, I popped open one of my folders and read through about 20 of 75 stories. In the folder view they looked greyed out and the story count had gone down. However, when I returned to the top level view where it lists all your folders, I hit the refresh button at the top and every story I had just read refreshed back to the ‘unread’ status.
If I use the menu in the folder to Mark All as Read, this does not happen.
It seems like the app is not syncing read status of stories at all, unless I use Mark All as Read.