When you have nested folders, marking a child folder as read does not update the count for the parent folder.
Say you have parent folder P1. Within it are children folders C1 and C2. C1 contains feeds F1 and F2 and C2 contains feeds F3 and F4. P1 says there are 20 unread items because C1 has 15 and C2 has 5. I right click on C2 and click “Mark Folder as Read” and C2’s unread count goes away because it’s 0. P1, however, still says 20 instead of 15.
I’m pretty sure this is unrelated to the other topic I just posted about folder unread feeds being out of sync with the individual feeds, that’s a recent issue and this one has been going on for longer.