This is the effect of a mixed domains usage along with Joomla! configured with a hardcoded single domain URL. Browser won't allow scripts to work across different domains such as http://mysite.com and http://www.mysite.com, thus for security policy scripts are blocked accordingly.
Normally Joomla uses dynamic base address for the site, having a look at the Joomla configuration.php you can check that the variable named '$live_site' has empty value as by default.
Keep in mind that you should always use only 1 domain for your website to have good SEO, so it's recommended that you redirect from one domain to another using the htaccess.