When I go into "Show new replies to your posts", I'll see that there are 5 there (using an arbitrary number). I'll click on the "New" button for one of them, read it, then click on "Show new replies to your posts" again. Suddenly there is only 1 post in there now and I don't know what I've just missed.
It does this is the boards themselves, too. I'll click the "New" on one I've read but haven't commented on, then return to the board, and the ones next to that particular thread no longer have the "New" button next to them when I haven't read them yet.