Code changes don't take effect

Code changes don't take effect

Hello,

I have the same template on two websites (WordPress). I downloaded a Custom Javascript plugin and added the following code:

Code: 
$("#wrapfirst").removeClass("fadeInUp pagewrap1");
$("#wrapsecond").removeClass("fadeInLeft pagewrap2");
One website applied the changes and the other didn't. The one that did is  www.shawneegaragedoors.com  and the one that didn't (still has fadein effects) is  www.madisongaragerepair.com

I also tried a different thing that worked on the Shawnee website but not on the Madison one. I deleted the following from the custom.js file:
Code: 
//CSS Animation
jQuery(window).scroll(function() {
	jQuery('.pagewrap1').each(function(){
		var imagePos = jQuery(this).offset().top;

		var topOfWindow = jQuery(window).scrollTop();
			if (imagePos < topOfWindow+400) {
				jQuery(this).addClass("fadeInUp");
			}
		});
	
	jQuery('.pagewrap2').each(function(){
		var imagePos = jQuery(this).offset().top;

		var topOfWindow = jQuery(window).scrollTop();
			if (imagePos < topOfWindow+400) {
				jQuery(this).addClass("fadeInLeft");
			}
		});
	 
	 jQuery('.postwrap3').each(function(){
		var imagePos = jQuery(this).offset().top;

		var topOfWindow = jQuery(window).scrollTop();
			if (imagePos < topOfWindow+400) {
				jQuery(this).addClass("fadeInRight");
			}
		});	
		
		
});
	
jQuery(document).ready(function() {
  	jQuery('.srchicon').click(function() {
			jQuery('.searchtop').toggle();
			jQuery('.topsocial').toggle();
		});	
});
Then, I deleted
Code: 
.pagewrap1, .pagewrap2, .postwrap3{ visibility: hidden;}
from the style.css.

In both cases, only the Shawnee website changed.

Can anyone help me out with this? I can't seem to figure it out.