Can you tell me exactly what you're seeing?
Here is what we do and why:
always adds itself to autorun on install for the current user, and removes it on uninstall
users can disable autorun using "task manager > startup"
should never start twice - we prevent this from happening
Also since the f.lux corporate build installs for all users on the machine, it does add a toggle to options. Any user can opt out of autorun, and f.lux will remember the setting. But we do not do this for single users because they have two ways to do it already: uninstall, or use task manager.