Right so you are using @MaxZieb 's hypeDocument.scrollToSelector extension Same page scroll using Hype buttons - #11 by MaxZieb and not the smoothscroll.min.js library
You are running a bit of code to ensure you always go back to the top of the page after returning to that scene.
window.setTimeout(function () {
document.body.scrollTop = 0; // Safari
document.documentElement.scrollTop = 0; // Chrome, Firefox, IE and Opera
}, 0);
But this is clashing with your scroll code running at the same time and effectively gets cancelled out.
The simplest thing I can think of is to wrap the scroll code in a timeout. allowing the document.documentElement.scrollTop to complete first.
window.setTimeout(function () {
hypeDocument.scrollToSelector ('#Scene3_Marker02',2);
}, 10);