Not sure I might have understood you fully - so bear with me if I haven't.
It takes the 'new' flag off based on whether you have looked at the post. In the case of flat view it assumes all 'new' in that thread. In threaded view it does it one by one. It isn't based on time while you are logged in. If you log out it assumes that you have read all you want and sets the time for 'new' to the last one that you would have seen last time you were logged out.
At least that is what I recall it doing. It was a while ago that it was written.
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'New ' Posts new
'New ' Posts new