Tom,
It appears that when you create the static header that the menu gets pushed to the very top of the page causing it to be hidden beneath the header.
I don’t know if it is the right way, but I was able to get it back using the following code:
.site-header {
position: fixed;
z-index: 2000;
top: 0;
width: 100%;
}
.main-navigation {
position: fixed;
margin-top: 100px;
z-index: 2000;
width: 100%;
}
.container {
padding-top: 150px;
}