@twocables Great! That seems to have fixed it! Thanks a bunch!
You're welcome. The reason why it fixes it is, having f.lux in the Startup folder is identical to just double-clicking a shortcut to f.lux after Windows starts. That's how the Startup folder works.
When you install f.lux, it doesn't place a shortcut there because it creates an entry in the Registry for its startup because it uses a special command in the Registry called "NoShow" to keep the f.lux window from opening on Windows startup.
So, if it stops starting with Windows, then somehow that Registry entry was deleted. Usually, the only way to get it back is by reinstalling f.lux. Putting it in the Startup folder will only run the shortcut. To see what I mean, create a shortcut to f.lux and just double-click it. That's the same thing, only you're running the shortcut manually. The Startup folder runs shortcuts for you automatically, but it's not anywhere near the same thing as the way f.lux gets itself to start up with Windows without its window opening (that is, with the "NoShow" command in the Registry).