Plugin author here, I can help clarify that. The scrolling is throttled so that all the checks aren't run with every single scroll event, as that would choke everything. So the small delay you see there is some 0-100 millisecond value while it hasn't triggered the event yet.

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.