You have for your header a -20px value for the top attribute. This causes the header to go up -20px, creating this extra space.
This is located in templates/protostar/template.css on line 14113
Now, removing this top: -20px; will give you an extra space on top of the header. If you don't want this, then you have to adjust the padding for the container class - templates/protostar/template.css on line 14169.
.body .container { background-color: white; -moz-border-radius: 4px; -webkit-border-radius: 4px; border-radius: 4px; padding:20px; **/* Change this to padding: 0 20px 20px; */** ... }
Change padding to padding: 0 20px 20px;
.navigation{margin-top: -20px;}