I recall that the site has some flamewar detection algorithm that will penalize a story if it detects a flamewar. I don't have a source for this at the moment, though.
"In order to prevent flamewars on Hacker News, articles with "too many" comments will get heavily penalized as "controversial". In the published code, the contro-factor function kicks in for any post with more than 20 comments and more comments than upvotes. Such an article is scaled by (votes/comments)^2. However, the actual formula is different - it is active for any post with more comments than upvotes and at least 40 comments. Based on empirical data, I suspect the exponent is 3, rather than 2 but haven't proven this."
"In order to prevent flamewars on Hacker News, articles with "too many" comments will get heavily penalized as "controversial". In the published code, the contro-factor function kicks in for any post with more than 20 comments and more comments than upvotes. Such an article is scaled by (votes/comments)^2. However, the actual formula is different - it is active for any post with more comments than upvotes and at least 40 comments. Based on empirical data, I suspect the exponent is 3, rather than 2 but haven't proven this."