You should check that it is displayed only when the first page loads, and not on internal links to the site. I like using jquery for this kind of thing.
if ( document.referrer == null || document.referrer.indexOf(window.location.hostname) < 0 ) {
$("#logo").animate({
marginLeft: "100px",
easing: 'swing'
}, 3000 );
} else {
$("#logo").css({ marginLeft: "100px"});
}
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