I figured the problem.It was W3 total cache.I deactivated it ,now its fine.
But can some one help me in figuring why that happened with total cache?
Thanks in Advance.
It was assigned to primary menu.But still the same.
This problem since we installed W3 total cache plugin.
You can add custom CSS like this
.site-header{
margin-top: -33px;
}
You can change the the value to what ever you want.