You may have discovered the solution by now, but I happened across this thread because I lost my tray icon recently due to some system tinkering to resolve Windows 8.1 upgrade issues.
Try this commonly overlooked procedure:
Right click your task bar.
Open Task Manager.
Click the Startup tab.
Check the status of avast! Antivirus.
It will probably be disabled. If so, select it and click Enable button at bottom.
Exit Task Manager.
Reboot and enjoy.