Performance in JavaScript is slow, as you're going through many layers of abstraction to get any work done, and many manipulations with objects on the screen are happening in the background. Performance cannot be guaranteed from system to system.
You'll find that with all jQuery animation, you will get a higher "frame rate" (not the right term here, but I can't think of a better one) on faster machines and better-performing browsers (such as Chrome) than you will on slower machines.
If you are curious what all happens in the background when you set a scroll position, or other property, use one of the many tools for profiling your code. Google Chrome comes with one built-in, and for Firefox, you can use Firebug to give you some insight. See also this question: What is the best way to profile javascript execution?