When you say near the beginning of sex scenes, they wouldn't happen to be right as an animation of some sort starts, would they? Usually that's a case of the video being called, but not actually loading immediately, resulting in it removing the current image and showing the one below for a brief moment before the animation starts. Ren'Py isn't great at playing video, but I hear there's some new updates out that help with that, so I'm looking into converting it at the moment.
Which version of Ren’Py did you use? Which version of Python did you have installed when developing?
No, they are 10-30 frames into the animation which makes me think it is a different type of error. Moreover, the onion issue behaves in a way that is not specifically graphically related; loading an older save, where no onion was available causes an onion to appear graphically properly, but illogically.
Another possible issue was that when I traced back to an older save the options in saving the childhood friend leading to non slave routes were available briefly, but then did not work later down the line in the following scenes. However, this may be intended behavior as perhaps earlier choices would have lead to “better” outcome, and the scenes where identical for narrative purposes. (Basically, from saving Riley to the next day, no matter what choices are made in my game, she is punished at night, and I do not seek her in the morning).
I did notice that for whatever reason, your game did not end up using the GPU, unlike the games which did not have a problem on my machine.