"To clerify, the problem is that certain icons show up in the list for choose-icons, but then do not show up in the tray itself. Correct?"
Correct. But it's only the system icons like sound, network, battery life.
When I select 'show all icons', all icons are displayed properly, including the system icons that I mentioned above. But when I uncheck that box, the extra icons dissapear including the ones that are supposed to be displayed. FYI, I did reboot.