This is expected behaviour. There is no way to disable notification updates when opted into background updates, unless you host the background update files locally. Normally, when opted into background updates, the machine is updated via background updates as the background update check occurs more frequently (once per day) than the notification update (once every 7 days), however, it's not unusual to have the notification update display when opted into background updates, instead of being updated silently.
If you're licensing Flash Player, you can host background updates locally and prevent the update notification from displaying. Information on hosting background updates locally is found in Chapter 3 of the Flash Player Administrator's Guide.