OK, you are talking about the hidden icons or the old System Tray...
Normally in Customize, all the icons are available for showing or not showing in the tray, but they should be there so you can select an option. Some settings that might effect this is the Turn system icons on or off, so try to turn them on. If that doesn't work, perhaps the "Restore default icon behaviors" would help.
If it isn't one of those, I would have to think something had overridden your normal behavior.