Oh that's not about the scrolling, that is a graphical issue relating to alpha masks, which are only used in the game for the onion animation.
One potential fix though, press shift-G in game, and change the renderer to angle2. After that, close the game and try again. I've heard this fixes it in most cases, but I'm unsure what other effects it has. The flickering issue is unfortunately hardware specific as far as I know.