Document ready can not be used with jQuery Mobile because of how jQuery Mobile handles page loading.
To find more about page events, its difference to document ready take a look at this ARTICLE or find it HERE.
Working jsFiddle example: http://jsfiddle.net/Gajotres/CPpBD/
Basically all you have to do is change this:
$(document).ready(function () {
$('.flexslider').flexslider({
animation: "slide",
animationLoop: false,
itemWidth: 80,
itemMargin: 5
});
});
to this:
$(document).on('pageshow', '#index', function(){
$('.flexslider').flexslider({
animation: "slide",
animationLoop: false
});
});
You can read more about pageshow event in a link I posted at the begging of this answer.