First, get rid of getApplicationContext(). You almost never need it and it is frequently the wrong choice. Replace it with this, since whatever you are calling getApplicationContext() on is a Context.
In the code you have listed, you never raise a Notification. Hence, it is difficult to help you figure out why you are getting more than one. Calling cancelAll() on the NotificationManager should get rid of all outstanding notifications from your application.
My best guess is that onDestroy() is not being called on your service. That would occur if something else is keeping the service in memory (e.g., you have an active bound connection to it via bindService()). Or, possibly, you have something strange in your <service> element in the manifest (e.g., an unnecessary android:process attribute) that is fouling up the NotificationManager cancel() operation.