I installed Netrunner Rolling 2016.01 and does not work center notifications. Notifications are displayed on the desktop but the notifications do not save icon in the Notification Center.
That would depend on what application notifications your expecting to stay in the notification area of the widget.
The settings for notifications would need to be turned on and/or set up inside each application that support this feature.
For applications still based on QT4 you may need to install sni-qt and/or lib32-sni-qt (32bit lib for 64 bit systems) if it’s not already installed.
NOTE: Some applications use notifications others do not and not all are persistent notifications.
You could try removing the notification widget from the panel and adding it into the system tray to see if that helps, some application notifications will not stay in the notification area when it is a separate widget and not part of the tray. This would also depend on the application that is sending the notification.