I have implemented push notifications for my app with customized layout.When app is in foreground and notification came everything works fine and layout of Notification is showing as i created. But when application is in background then Custom UI of the notification does not show up but it shows some default UI of notification.
It is a bit hard, to figure out your problem without code samples, but did you use RemoteViews?
When I tried what you are stating in your question I experienced a simular problem, because I didnt use Remote Views in a proper way.
I hope I could help you out :)