this is a problem with using an embedded PDF.
the embedded PDF is not natively supported in most browsers and will rely on a third party plug in to be installed.
to embed the PDF, you need to use the <object> tag. Put bluntly, the object tag punches a whole through the page layout. CSS styling and DOM layering cannot be applied to the object tag.
There is no standards compliant why to embed a pdf document into a web page that work in all browsers.
the only work around i can think of would be to add the PDF to flash object, when embedding a flash object, there is the wmode transparent option to help work around z-index layering issues with flash.