I had this on my system. After booting, the tray icons did not load.
I have disabled the "hide inactive icons settings" therefore this could not be the problem.
After some research in the internet i found the sollution here:
Tray-Icons missing - how to fix (http://tray-icons%20missing%20-%20how%20to%20fix)QuoteThis is caused by a timing defect in the Windows function Shell_NotifyIcon in shell32.dll, which has a timeout fixed at 4 seconds. Combined with an unfavorable Windows API message this causes the problem, which befalls many heavily loaded computers that don't have ultra-fast hard disks. Changing the timeout to one minute and removing the unwanted message solves the problem,
This means the shell32.dll needs to be patched (there is a patch on that side).
Also the other sollution works, you can just log off and log on again and you get all your icons.