I have a problem using the CSS produced from themeroller

My pages do not look the same after changing a theme and to try to solve this problem I imported jquery 1.3.1 from

http://jquerymobile.com/blog/2013/04/10/announcing-jquery-mobile-1-3-1/

I then imported this file into

http://jquerymobile.com/themeroller/index.php

and immediately did a 'Download theme zip file'. After comparing both files I noticed quite a few differences.

Why are these files not identical?