More than one banner in Notification Center
I think your issue is with the behavior of banners versus alerts. 

Banners by design appear for several seconds and then disappear.
Alerts are designed to stay put. You can change the way an application's Notifications behave in the Notifications Preference Pane.

So switch your app's behavior to show alerts instead of banners and you should be fine.

Unless, of course, I'm misunderstanding your question.