My CIS, which had been behaving nicely, has taken to not posting its icon in the system tray after boot-up. Task Manager reveals that it is active. If I run it from the START button, it reports that everything is cool, and /then/ places its icon in the tray.
I have this issue occasionally also. I too believe it is a Windows issue. What you are (not) seeing is the GUI. The actual engine is active and protecting your computer. Running the App from the START button, or even your desktop if you have placed the icon there, will restart the GUI in the tray.