Date.getTime() not including time?

What milliseconds? You are providing only minutes information in the first example, whereas your second example grabs current date from the system with milliseconds, what is it you're looking for?

String date = "06-04-2007 07:05:00.999";
SimpleDateFormat fmt = new SimpleDateFormat("MM-dd-yyyy HH:mm:ss.S");
Date myDate = fmt.parse(date);

System.out.println(myDate); 
long timestamp = myDate.getTime();
System.out.println(timestamp);

Because simple date format you specified discards the milliseconds. So the resulting Date object does not have that info. So when you print it out, its all 0s.

On the other hand, the Date object does retain the milliseconds when you assign it a value with milliseconds (in this case, using new Date()). So when you print them out, it contains the millisecs too.

Instead of using the Sun JDK Time/Date libraries (which leave much to be desired) I recommend taking a look at http://joda-time.sourceforge.net.

This is a very mature and active sourceforge project and has a very elegant API.