My "solution" has been to use a browser that doesn't reload a page when you return to it ... so I bring up the new threads search, and then click back to it when I'm done reading and/or posting to a thread. It keeps the state of the new thread markers static.
Of course, if I accidentally click the close box, I'm screwed because I lose the markers.
It's not elegant, but it works.
I've also had to resort to logging out and then using the "view today's active threads" hotlink on the main page.
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