There are so many possible reasons it isn't really worth exploring. But most likely it's simply because someone died earlier in your first run, compared to your second. And that could be because the "wrong" person was targeted by the stun, or because a debuff wasn't resisted, or because a critical hit landed at a bad time, or etc etc etc.
Adding to Kram's explanation, this will be an especially prevalent issue in teams that aren't speed tuned which is pretty common early on in our account. Scyl is another wrinkle in that she'll be putting out speed boosts at random, which will affect our turn ordering.
Affinity could also be another common issue.