When scrolling down the page, there seems to be extra padding above the logo that is throwing off the alignment with the rest of the site. I've been trying different solutions to correct this issue:
//$('.navbar-brand').css({ 'padding-top' : 0 + "px", 'padding-bottom' : 0 + "px" });
If you'd like to take a look at the website, you can find it here. Just keep in mind that the problem only occurs when scrolling up or down on the page.