> I don't recall ever seeing it when the story was positive
... is just sample bias. By far most cases of this are positive stories. Indeed most are blog posts written by the companies themselves. Sometimes they even complain and think we're biased against them, which of course is not true, just sample bias again.
Re the story rank: users tend to flag stories that have a high controversy-to-substance ratio, and moderators penalize such stories. In the case of negative posts about YC or YC-funded startups, our policy is to penalize them less, not more. But that doesn't mean we do nothing. Why? Because the heat of indignation guarantees massive upvotes. There needs to be a countervailing factor or such posts would fill the front page every day. It's a balancing act.