What web browser are you using?
For reference, I'm using both IE6 & IE8 and I don't lose the new flags.
If however you only pop in and read one or two posts, and you leave some new ones until you come back later in the day, those ones you've left will get marked as read and the only new posts that get flagged are the ones from the time you logged out and left the site. This is something that's always happened, both on here and HJ.
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