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The following list is a set of notifications about stuff you're following or that concerns you (replies, mentions, etc).
The notifications remain, but are marked as 'read'. New notifications for things that are unread get marked 'new'.
Notifications remain so that you can find older stuff you interacted with easier. It makes a lot more sense over time, when you're there wondering where that thread is that you took part in where @someone said something to you a month or so ago.
Velocio
Mule 
Is the 'following' list meant to clear once you've read things? Loads of threads I read yesterday which have not had new posts are still there.
Also, I used to have the forum settings so the last post was first, wish that was an option again. I can't deal with all this scrolling.