Sorry
The only thing I can think of is that You can mark series and seasons as watched. I think I've had to do that for some series that behaved as You described sometime long a go.
Yes I can do that, but since I filter out episodes that has not yet been aired, I don't want to make those episodes marked as watched.
The idea with my unwatched filter was that I only want to see series that actually has real episodes to view.
I am not interested to have "Lost" present in my unwatched view since there are no epiosdes to view just yet.