Since I lasted reported this problem, it got fixed and works in WebKitGTK 2.38.x. However, in in 2.39.x, it's not working.
Not sure if they're the same problem, but kinetic scrolling doesn't work in Reddit post popups and lots of other places.
I'm very excited to say that this problem can no longer be observed as of WebKitGTK 2.39.9