I think there are conflicts between Waypoint and jquery.onepage-scroll.js Plugin. If I were you I would switch to a plugin that has more option, I've used FullPage.js
there are way more options and you can do anything you want like this where you can add custom animations.
you can use afterSlideLoad
to do whatever you want once you slide to a cetain page
afterSlideLoad: function( anchorLink, index, slideAnchor, slideIndex){
//first slide of the second section
if(anchorLink == 'secondPage' && slideIndex == 1){
alert("First slide loaded");
}
//second slide of the second section (supposing #secondSlide is the
//anchor for the second slide
if(index == 2 && slideIndex == 'secondSlide'){
alert("Second slide loaded");
}
Hope that helps.