Whew, I found the bug. This was a regression I introduced in March while cleaning up NewsBlur’s feed loading code to make the many feed queries faster. That worked, but it caused unread pagination to depend on a changing set of unread stories. As items were marked read, the page boundary could shift, which made some unread stories get skipped until you reopened the feed.
I fixed this for both individual feeds and folders. Sorry about that, and thanks for the clear report.