JeeLabs Precision RTC Module

You don't seem to be decoding the BCD in the code above... What about:

var seconds = ("0"+data[0].toString(16)).substr(-2);
var minutes = ("0"+data[1].toString(16)).substr(-2);
var hours = ("0"+data[2].toString(16)).substr(-2);
rtcTime = (hours+":"+minutes+":"+seconds);