Could be that the event has enough time to send in Mozilla, but not in WebKit.
Try using hitCallback which will wait until the event is sent before the next page loads:
jQuery('.ga-track-isa').on('click', function(e){
e.preventDefault();
var theHREF = jQuery(this).attr('href');
_gaq.push(['_set', 'hitCallback', function(){
window.location.href = theHREF;
}]);
_gaq.push(['_trackEvent', 'media', 'download', theHREF]);
});