Used to have this issue as well, can't really remember the exact thing that fixed it, though basically I have a separate Bonus Game layout (which I'd assume you have as well, cuz of the Manual timing stuff) and all of my comparisons are set to "Personal Best" and timing methods to "Game Time" for the "Splits" and "(Detailed) Timer" sections in said layout.

The Simpsons: Hit & Run

Livesplit Help For Bonus Game

WWE Smackdown! Here Comes the Pain

Slime Rancher