The repro can be found here - http://jsfiddle.net/desandro/VQM7x/ - none of the rects should move when scrolling that container. Note that safari "stutters" on that test case, I believe this is related but slightly different issue. For chrome, this was solved by avoiding overflow on the repaint rects - https://bugs.webkit.org/show_bug.cgi?id=84979. Its likely that overflow in a different place may be causing that same behavior for Safari.
http://trac.webkit.org/changeset/117032
This seems to have been magically fixed on recent builds of chromium (bisecting didn't give enough information to narrow down what may have fixed it). I'll mark it as resolved, please feel to re-open if its actually not fixed.