One of my favorite things to do in this game is to watch check swing replays. It has to be the most flawed system in the entire game, next time you are playing please just go take a peak on some of the check swings you won't regret it.
Swing animations have nothing to do with the call, it only factors in the discipline stat and somewhat user input.
Whatever factors, it is incredibly messed up. There are times I just wish I could stop check swinging. I do it unconsciously at times.