May I see your URL please? You may have some dynamically resizing elements on the page that cause the misalignment or some extra paddings/margins.

first two menu items are the working links that are not aligning

if you look at the first two items this is how i put the URL: http://masjidalrahman.com/new/#welcome with smooth_scroll

they dont align but they smooth scroll

the next two i just put #welcome in the URL with smooth_scroll

these align but they do not smooth scroll

First off – congrats on the website, looking great.
Do you want the anchor positions to be higher then where they actually take you at the moment? Can you try without the slider see if the links go higher? I presume the Rev slider might cause the misalignment as it loads at run time…

moiz41510 – same case here, pls test without the slider, if the positioning is more precise and we go from there.

At the moment the anchor positions need to be a lot lower then where they are at the moment they are stopping a fair way above where they are suppose to. I have removed the slider and still hitting same positions. Like @moiz41510 sates, the problem occurred when I put the smooth_scroll in the link relationship.

Thanks

Find this in your js/common.js :

smoothScroll.init({
		selector: '[rel="smooth_scroll"]',
		selectorHeader: '#header.sticky_header', // Selector for fixed headers
		speed: 500, 
		easing: 'easeInOutQuart',
		updateURL: false,
		offset: 0,
	});

Play around with the offset to see if that can do the job for you…
You can also comment out the selectorHeader line to disregard ignoring the sticky header height.

Thank you