I was messing about with Gnome Fallback/Flashback, it's fun but not what I wanted so I swapped back to Default Ubuntu Gnome Desktop. The stuff I have running no longer appears up in the top panel. I would normally see Variety, Steam, PIA and Insync up in the top right next to the regular applets. These programs are still running but they are not showing up in the panel.
Images to show what I'm talking about
Also asked on the Ubuntu forum here https://ubuntuforums.org/showthread.php?t=2403720