You need to put all your javascript in the section of the chapter AFTER you enable jQuery, but BEFORE calling jQuery mobile.
Your head file should look something like this (custom JS in the second file):
<script src="http://code.jquery.com/jquery-1.7.1.min.js" type="text/javascript"></script> <script type="text/javascript" src="http://www.example.com/path-to-file/custom-javascript.js"></script> <script src="http://code.jquery.com/mobile/1.1.1/jquery.mobile-1.1.1.min.js"></script>
UPDATE
In the link to the page, add the attribute data-ajax="false" . If you want to disable Ajax navigation throughout the site, enter the following code into your custom JS file:
$(document).bind("mobileinit", function(){ $.extend( $.mobile , { ajaxEnabled: false }); });
Here's a link to the docs: http://jquerymobile.com/demos/1.1.1/docs/api/globalconfig.html
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