From the Knowledgebase

My Theme's menu bar or header obscures the full screen view of the PDF

To ensure the menu is behind the viewer when in full screen, you could try adding the following CSS to your theme's style.css or similar:

.pdfemb-fsp-wrapper {
   z-index: 999999 !important;

You might need to increase the number to something even higher to ensure it takes priority over the 'z-index' of your Theme's header.