For a time difference, note that the calendar starts at 01.01.1970, 01:00, not at 00:00. If you're using java.util.Date and java.text.SimpleDateFormat, you will have to compensate for 1 hour:
long start = System.currentTimeMillis();
long end = start + (1*3600 + 23*60 + 45) * 1000 + 678; // 1 h 23 min 45.678 s
Date timeDiff = new Date(end - start - 3600000); // compensate for 1h in millis
SimpleDateFormat timeFormat = new SimpleDateFormat("H:mm:ss.SSS");
System.out.println("Duration: " + timeFormat.format(timeDiff));
This will print:
Duration: 1:23:45.678