Of course, with any update, there must be winners and losers, because there are only so many opportunities for visibility, and lots of competitors :)
I don't think you will find a "secret" as to why some are affected and others are not, because there are very diverse sites in both categories.
Part of the reason for this is that Google's system is by no means perfect. Let's say they aim to target people that run robots to comment spam. They are likely to get some of them, and perhaps even the majority - but that doesn't mean they 100% eliminate comment spam bots. So, there will be some people who use comment spam who benefit.
That said, the more 'edgy' the techniques you use, the more likely you are to see large fluctuations in search results - that's my experience, anyway. If you want long term growth, you need long term techniques and you will be much more immune to update problems. If you want fast growth, then you also need to expect a quick fall.