You are using wp super cache plugin, which is why you only see the problem in chrome. You need to clear it’s cache for all pages to update. And probably clear browser cache too.
Actually it looks the same in firefox, safari, and chrome, all heights are shortened.
See my screenshots
Please see screenshot of my firebug console.
You can notice that a script has added
position: relative; z-index: 5; height: 131px; to
position: relative; z-index: 3; to many other subsequent Div tags
If you look at my screenshot, I am using header #3
You can see that there is no additional style codes to
<div class='header-wrapper'> or subsequent Div tags.
By looking at the codes, I have no idea which plugin is causing this conflict.
Please disable plugins one at a time and disable your super cache to find the conflicting plugin.