Well, to begin with, I'm pretty sure the game does not try to capture every event when a pitcher throws over to first base (that would be annoying, after all), so either a pickoff attempt is successful or it results in an error, sending the runner to second base. (This, at the very least, is how I believe it works based upon my own experience. And not true with catchers throwing to first, which is a more rare event and often results in the runner getting back safely. I'm also not speaking to all of the times where you as a human manager call for a pickoff.)
And my other thought is, sample size, sample size, sample size. I've been playing out all the games for my team in my fictional league (see below in signature) and I don't sense anything that seems to be out of line with what you would expect in real life. Doesn't mean I'm right. But this smacks of perceptions based upon small sample sizes and the very human reality that we over-emphasize events that punish our team, less frequent outcomes that hurt us, over events that go in our favor.
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