However I think this is more due to the generous use of drop shadows than the javascript.
You can change the throttle by setting $.waypoints.settings.scrollThrottle = 50, or whatever number you like, to try to reduce flickers in cases like these. Just be aware its a balance you'll be striking with executing more scroll checks. But all the selectors and offset values are cached so the performance should still hold up should you choose to lower this value.
If I notice it, then by definition it is too bad.
Just tried with the webkit inspector, if you remove all the box-shadow, the page is smooth.
What, you were expecting the first code they wrote to be perfect?
I very much disagree. It's an awesome way to capture the reader. I love it myself, not needed reloads, hunting for 'next' buttons, ... Yes you lose the relative position on the page indicator from the scroll bar, but it's irrelevant by the time you get to the bottom of the page anyway.