Those stories fell off the front page because of software that penalizes overheated threads, which tend to be shallow and sensational. That software has been running for years.
Even if an automatic penalty hadn't kicked in, moderators would have penalized that first link (even if we personally agree with what it says). First, it's a duplicate that adds no new information over previous incarnations of the story (which have already appeared more than once on the front page, already an indulgence and certainly not a pro-MS one). Second, it's a garden-variety riler-upper, and those aren't a good fit for HN, as should be well known by now.
None of these mechanisms has anything to do with Microsoft. I'm pretty sure that the bias you're arguing for doesn't exist at our end. How sure are you that you're not simply noticing things because they fit your interpretation?