I'm using a Surface Book 3 at 59Hz, so I don't think it's that. I've played several other Ren'py games that didn't have this issue, but after leaving this comment I played another game that was doing the same thing, and I found a workaround - the flickering only happened when it was set to fullscreen, so I switched to windowed mode and just maximized the window, and that fixed it. Thought I'd let you know in case other people run into the same thing.