You need to set a value for the badge
key in your push notification payload. From your description, it sounds like it is only your application which is updating the badge number, and not the notification itself.
See The Notification Payload of the Local and Push Notification Programming Guide for details:
Keys and values of the aps dictionary
badge
(number): The number to display as the badge of the application icon. If this property is absent, the badge is not changed. To remove the badge, set the value of this property to 0.