It might be caused by the location of the judgments in the play. Several factors could make a difference.
The misses in the S play could have been more spread apart compared to the A plays.
The 200/100/50 in the A play (in strings that weren't bad enough to set the Bonus value to the lower cap) could have been more spread apart compared to the S play. A long string of bad judgments that set the Bonus variable to the lower cap is similar to a miss in that regard (it's better to have one very long string of bad judgments, compared to 2 long strings of bad judgments with a recovery in-between).
