It was mostly at the beginning of the game.
And the skip button went too fast so I tried to back up a lot... it may be a problem with the scene changeover.
The start of this game is very different from typical visual novels, so I assume they might be programmed differently?
I use Windows.
And the quick menu.
I've played it further now, and it looks like it's the beginning parts that's problematic.
Once it turns into the normal style visual novel the problems seem to vanish. (I think.)
So it could be something with whatever coding you did for the first part of the game. (The comic-book intro and whatnot.)