Had a problem with some of the icons in my system tray failing to appear on Windows start-up. Never experienced this kind of weirdness before.
The Mysterious Case of the Disappearing Icons began shortly after I uninstalled all the programs I no longer use (something I do every 3 months), and then scanned the registry to delete unnecessary entries (thousands).
Afterwards, my system *did* start noticeably faster. Maybe too fast.
The only thing that worked was to find (& install) a program that delays the loading of Windows programs on startup .. called (what else?) » Startup Delayer (freebie).
Impressive little program. It comes with a graphical interface to delay the startup of your programs (via drag-n-drop functionality) .. for up to 2 minutes .. which should be plenty for most users.
Some programs will insist on starting with Windows .. no matter what kind of delay you assign to them in SD. I had 3 such rebels (including Daemon Tools & DAP), which I re-configured to NOT Start with Windows. I now start these manually, as needed.
Many of the sites I consulted theorize that too many programs are trying to load concurrently, which prevents some of the tray icons from appearing.