Although I do feel there is some bug with the randomness that causes streaks of repeat events (like passed balls, hit batters, etc.) perhaps in your example there is another explanation that may also be affecting the results.

If a pitcher does not allow a baserunner after he goes to BFA 0, he is not downgraded even if they use up all there BFA. In other words, Cook could start an inning with -3 BFA and until he gives up a hit (or maybe a walk?), he won't be any more likely to give up hits than he was when he still had 1 BFA left.

At least that is how I understand it based on a post by Mike Bravard in this forum. I'm sorry to say I forget the post. If I find it, I'll mention it - but maybe you knew all that.

Good luck,

Dave