Looking back on my more recent experiments with OBS, one of the funniest / stupidest things I've done as a fix is add a single undetectable pixel that uses keyframe animation to move across the edge of an animation.
Far as I can tell Clip Studio Paint won't export every frame of an animation unless every frame is updated, and OBS doesn't seem to render frames where nothing is updating, which causes this effect where it stops rendering and then starts rendering again too late, dropping a bunch of frames in the process. I understand the technical reasons why both these things are true, and how normally they would be a good thing, but this is the only way I've been able to make sure animations play, and in some cases layer on top of each other, properly.