Type about:config in a new Firefox window, when you get a warning popup, click "I'll be careful, I promise". Now you have 4 columns of information, one entitled Preferred Name
I forget now what preferred name I searched for, but I changed the setting from =0 to =1, and after a reboot, my missing icons were now showing in the notification area on the bottom right, as they used to.
I just noticed only a few icons are no longer in my notification/lower-right-corner-tray-area: Skype, MSE, and my memeo backup external drive.
In "Customize notification icons", my skype is set to SHOW.
MSE (Microsoft Security Essential) isn't even in the "customize notification icons" window under past items, so I can't toggle the notification setting). My last update to MSE was 4 days ago KB2754296, and I'm wondering if that caused this problem
My Memeo instant backup icon now appears represented by Safely Remove Hardware and Seagate Dashboard.
Skype MSE, and my backup are indeed running.
When I show all icons, there are 10 (volume, network/LAN, battery, synaptics pointing device, camera assist sw, acoustic silencer, safely remove hardware, seagate device, spybot, and openoffice). I hadn't paid much attention to many of these, but is there a 10 icon limit?
I tried rebooting to no effect. Do you have any other ideas how to get my missing icons back?

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic