I'm had the same problem, and the only solution I've found is to reboot.
I tried searching the forums but can't find the solution to this problem. I normally have several programs running on my PC at the same time so it's normal to have about 8-10 icons on my system tray. Most times when I minimize these programs I minimize them to the system tray to keep them out of sight but still be able to access them when I need to. At times, I will be using Explorer and receive an error that the program has to close. Whenever this happens it refreshes my screen but most of my system tray icons will disappear. How can I restore these? If I simply try to get to the running program by reopening it, I get two instances of the same program running. This gets on my nerves, because I have to reboot and restart my programs, causing me to lose what the program was originally doing.