I’d need to see the rendered page really to be able to inspect it properly.

Have you made any css revisions to the new site? If so remove the custom css to test if the margins move back. If they don’t, use a web inspector like firebug or chrome web dev tools to look at the header code to see where the margin is coming from.

I would imagine there’s something in there like this –

#top {
margin-left: 20px;
}

It needs to be

#top {
margin-left: 0px;
}

You can paste the css into the style.css at the bottom and save. Then refresh the page to see if this resets the alignment.