It happens because you removed fixed header width and used such a big logo.
The result is, a 100% width logo area, leaving the ad zone html, which gets push down a line and floated right = next to the search box.
Easiest solution, since you not have room up there for the ad anyway, remove the html
Code:
<div id="headside">
<div id="headbanner">{$zone_a}</div>
</div>
Second option, to just hide it, add to user.css
Code:
#headside {
display: none;
}