Unfortunately, this appears to be a Chrome bug. Specifically, it looks like you're running (and I could only reproduce this with) 125% zoom. If you resize the window, you'll likely see the double scroll flicker and not always be there.
This is likely due to internal rounding issues within Chrome. The simple presence of overflow: auto on the container triggers this. (And we do need that to ensure menus in this area don't become too tall.)