Not sure what you're alluding to and it's pretty hard to answer vague insinuations—in fact it's impossible.
I have no opinion on the matter, but clearly the OP is alluding to the fact that HN will bury negative stories about their investments.
The idea that HN "buries stories about [YC] investments" is one some people assume must be true—as you did, for example, in your use of the word 'fact' above. But the truth is the opposite. When stories are negative about YC or YC-funded companies, we moderate them less, not more, than we otherwise would. I've posted about this plenty of times, e.g. recently at https://news.ycombinator.com/item?id=13861389.
For example, consider the current post. This is not a good HN story, because it doesn't describe anything of intellectual interest. It also has a baity and misleading title, which breaks the rules at https://news.ycombinator.com/newsguidelines.html. But we haven't penalized it, and we haven't replaced the title other than to put quotation marks around "bribes", in response to a user's objection. Intervening less in such cases, even at the expense of HN's quality, is the price we pay for being able to answer comments like yours and the GP's in good faith.
I doubt these complaints pop up because of years ago, though. People just assume that's how it works whether it does that way or not, and confirmation bias does the rest, i.e. we notice the data points that match our assumptions much more than ones that don't. Plus it's fun to trade those with others who share the same view.
Say what you want about anybody else at YC, but Dan is one of the most trustworthy people in show business. If he says a story didn't get suppressed by the mods, bank on that.
I don't really doubt you tptacek, nor indeed doubt dang, but this is a problem with closed moderation we can't see whether YC manipulates the rankings to their benefit financially or otherwise and for those people who don't know you or dang personally there's little provable trust to be carried by such comments as you've made here.