The way HN is set up, having 500 comments would have contributed to that. The "flamewar detector" the mods sometimes mention seems to take comments/votes and comments/time into consideration then penalises threads.
Yes, this is correct from my observation, too. The comment-to-vote ratios go fast; up south, they will likely be out of the pages quickly. One might think that a post that falls off the homepage would linger on page 2 for a while, but it can be out of even the first 100 posts fast.
I have stopped thinking about HN's algorithms and just let it do its job.