In the last statement you are converting the duration to time which also considers the timezone. I assume that your timezone is +530, so 5 hours and 30 minutes gets added to 30 minutes. You can do as given below.
var eventTime= 1366549200; // Timestamp - Sun, 21 Apr 2013 13:00:00 GMT
var currentTime = 1366547400; // Timestamp - Sun, 21 Apr 2013 12:30:00 GMT
var diffTime = eventTime - currentTime;
var duration = moment.duration(diffTime*1000, 'milliseconds');
var interval = 1000;
setInterval(function(){
duration = moment.duration(duration - interval, 'milliseconds');
$('.countdown').text(duration.hours() + ":" + duration.minutes() + ":" + duration.seconds())
}, interval);