Please, it is important you let us know which version of IE you are using - I need more detail.
In IE8 using Compatibility View, the search input area is incorrect - it overlaps your NAV BAR. However, I saw no issues regarding misaligned boxes. It looks OK in FF.Click image for larger version.  Name: look.png  Views: 247  Size: 5.3 KB  ID: 10584

Regards,

jund - John Underwood