thanks for the feedback. Hope it can be solved soon.In my scene Shirou EP2, the Fade is triggered by McGruber Fade plug in, not the Overlay. So you can uncheck the Active box in McGruber Fade plug in in Atom Storyline.
I put the trigger in VAMSTORY or the Timeline in atom Storyline. I think this error is caused by low performance that the timeline failed to trigger the fade out order in time. I am testing the Mcgruber Relay and Delay plug in to check if it will help to solve this error while perfromance is low.