I'll need to do some searching again to locate it, but I recall reading a good blog entry from a developer that explained the process as Apple has designed it with regards to Notification Center and those display options. The bottom line seemed to be that, developers essentially get one shot (first notification) at trying to set those display options, but from then on, the end user has complete control over how they will show up from any app, or even IF they will show up. This is by design. I guess think about it, How much would it suck if a developer was able to continually change the NC options for their app to display an Alert style message (requires user intervention to dismiss) even if you chose to stop receiving those messages. No-one would like that, so poor user experience. I get it, even if it means it makes things hard for admins like us.
Of course, ironically Apple doesn't follow this same rule, as its almost impossible to stop receiving NC messages about updates to apps or the OS. I guess because… they're Apple and they can do what they want?
