It is difficult to pinpoint the cause of this without having a clearer picture of how the HTML5 shiv and jQuery files are being included in the document so this is a really a shot in the dark:
First of all, check if your HTML5 shiv is included into the document before any of your jQuery scripts that you're using to control HTML elements. If the HTML5 shiv is included after, then those HTML5 elements will most likely not be recognised.
Another thing you might want to try doing is to add a class or an ID to the new HTML5 element - for e.g. <nav id="menu">
so that you reference it as $('nav#menu')
or simply as $('#menu')
in jQuery.