How did you come to that conclusion? That is, how are you able to differentiate a story naturally being bumped off the front page by other stories getting more aggressive upvotes, and a story being buried by many flags?
If a story has 50 votes and was posted 5 hours ago, it should be ranked higher than any story that has less than 50 points and was posted more than 5 hours ago. If not, it shows that the story was flagged.
Also, Paul Thurott's http://winsupersite.com is completely banned from HN, most probably due to excessively being flagged for the crime of being a Microsoft watcher news site.
I don't think the ranking algorithm is that simple - I think it takes into account recency of votes, although I'm not sure. The first example does not seem suspicious to me, although the second one is surprising to me.
Watch articles that are critical of Apple or Google, or those are not critical of Microsoft, most of the time they get flagged down by overzealous fans.
I recall Paul saying on HN that he tweaks with HN's algorithm, and those changes are not represented in what's posted on arclanguage.org. In fact, he says it in response to that writeup: http://news.ycombinator.com/item?id=1781417 There's also the voting ring detector, which is not distributed.
It's more an observation that HN is highly skewed toward consumer Internet companies. And doesn't focus much on specific companies generally (Google, Apple, Twitter, and Facebook/Zuckerberg excepted).
Very few from this list: http://en.wikipedia.org/wiki/List_of_the_largest_technology_...
Do you have the raw ranking data available?