I have similar problems all the time. The list seems to be cleared at random. For example, I come to WP after a weekend offline only to find all posts are marked as already read. If they are not, I better get all pages of the list quickly, because it will surely clear itself before I manage to go through it. This is not the problem with the list itself, but with the posts losing their "unread" status without me even clicking on threads that contain them.
