This MS story from today also vanished from the frontpage quickly.
I contacted HN (you), I highlighted several vanished posts. You mentioned you see no pattern or unusual activities.
Also this one vanished: https://news.ycombinator.com/item?id=11846199
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?
There have been a lot of unfavorable stories about MS on HN, including recently. We don't do anything special to penalize them, nor do we let users abuse flagging in the way you suggest. In fact the Windows 10 update nagware saga has appeared numerous times on HN's front page, including multiple stories about clicking 'x' on the dialog box, how it screwed some African satellite operators, etc. The current one fell suddenly off the front page because of software (it set off the flamewar detector).
If MS "infiltrated" HN, it's news to me and I'd like to know about it. It's our job to protect the integrity of this place for the community and we take it seriously. When we see gaming and manipulation we crack down on it hard. But actually the BigCos aren't the ones who do such things. They're (rightly) too risk-averse.
If you think you see evidence of manipulation you should email us at [email protected]. When we get emails like that we always look into it.