Based on third-hand versions of events I've heard, it's a mixture of bureaucy (no one was ever fired for ranking Nature on top), (inter)national rankings ("I know this conference is better, but those are the rankings the funding agency sent us") and the amount of people willing to champion an issue in a board meeting. And then there's inertia: "This ranking got us good researchers so far so I see no good reason for changing it and devaluate everybody's publications".

I've never witnessed straight corruption, but I did witness marketing teams sent to prey on researcher's fears. So I wouldn't discount that too.