First run: 7.96% time penalty (796s over par)... 99959 / (1 - 0.0796) - 16000 = ~92600
Second run: 6.12% time penalty (612s over par)... 89750 / (1 - 0.0612) - 18000 = ~77600
So once you take the time and vitality out of the score and look at the points awarded for kills, you got 92600 kill points on the first run, and 77600 on the second, for a difference for 15000.
15000 happens to be the number of points that you are awarded for killing a boss. So what you ran into here is a bug where one of your boss kills in the second run did not award you any points. Although I have not personally encountered this, I have heard others who have complained that under certain situations, the topside boss during the split would not award points. This is most likely what happened to you.
First run: 7.96% time penalty (796s over par)... 99959 / (1 - 0.0796) - 16000 = ~92600
Second run: 6.12% time penalty (612s over par)... 89750 / (1 - 0.0612) - 18000 = ~77600
So once you take the time and vitality out of the score and look at the points awarded for kills, you got 92600 kill points on the first run, and 77600 on the second, for a difference for 15000.
15000 happens to be the number of points that you are awarded for killing a boss. So what you ran into here is a bug where one of your boss kills in the second run did not award you any points. Although I have not personally encountered this, I have heard others who have complained that under certain situations, the topside boss during the split would not award points. This is most likely what happened to you.