Quoting nakibest, reply 9
Missing icons is NOT a software malfunction, it is a Windows OS malfunction.
Missing icons in the notification area is a software malfunction, starting with Windows XP (I think) notifications are sent if the shell is restarting so applications are able (and have to for the icons to display) to refresh their handles and stuff.
No, it is a Windows OS malfunction. It seems to be happening when you have a lot of startup items. This is since WinXP, Windows 7 has it too, not sure about 8.
Minimizing those to under 10 or even 5 seems to help. But not all users can do this. And yes, it does not happen 100% reliably, for some users it is fine.
Also, it is different apps each time - sometimes one app is missing, sometimes another.
EDIT: You misunderstood. The problem with missing icons is when you power on the PC. When you restart the shell, ALL ICONS appear/come back, yes. That part is correct - the missing icons problem is on a full power down/restart ONLY.