Apparently submissions with text as opposed to URLs don't get ranked as highly. Two items submitted at the same time and with the same votes, one with URL, the other as text, the text one will rank significantly lower.
But that's my point -- there's all kinds of little nuances and "if X, then Y" in the system and hell if I have time to keep on top of all of it. To my mind, it seems a reasonable assumption that there is a mad sysadmin somewhere just screwing around with me. After all, in the past for most boards limiting voting or tweaking ranking or turning on or off features was traditionally handled by a person, not an algorithm. Maybe it's some super-duper cool collaborative voting checker that's working wrong or maybe somebody just had a bad day. As a user, beats me -- and once I have to start second-guessing who is doing what to me and why the site is totally screwed. In my opinion.
You shouldn't have to be on HN everyday and read all the pages to understand how the site works. That's an idiotic expectation.
By the way, I'm commenting on all user sites with non-intuitive behavior, not just the peculiarities of HN.
That might explain your observation.