Some apps use the old system tray. To view them in the elementaryOS tray edit /etc/xdg/autostart/indicator-application.desktop and change this line:
OnlyShowIn=Unity;GNOME;OnlyShowIn=Unity;GNOME;Pantheon;Now install the old panel indicator from launchpad.net:
http://ppa.launchpad.net/elementary-os/stable/ubuntu/pool/main/w/wingpanel-indicator-ayatana
After relog you should be able to see the icons in wingpanel.