I have taken a detailed look at your site. The problem is that when you reduce the width of the browser ( or view it on a lower resolution device ), the #main-container
centers itself with {margin: 0 auto}
BUT #header
remains static with a width of 1200px and therefore they both fail to align!
Reproduce how your iPad is rendering by reducing the width of your browser window (on your desktop).
I recommend making your header auto-resize & auto-center. You could start by reducing the size of the logo for lower resolution/mobile screens using css.
Otherwise, the site has a nice design.