I am in the same situation, trying to pop up a message on the notification bar (via eon_mobile_notification) but the message is not showing up if the app is in background, which makes it quite unpractical.
FYI: I have noticed that Android notifications behave differently than iOS ones. Which O/S are you referring to?
FWIW: I always send notifications in my mobile App's when they active in the foreground. I have not tried the background notification route. Sounds like it could be a bug. You might like to submit a Support Ticket for this.