Open the windows 10 task manager: Shift + Ctrl + Esc key. Alternatively the classic Ctrl + Alt + Del. You may also right click a blank area on the taskbar (where the clock and start menu is displayed) and choose the task manager.
Go to the startup tab and look for f.lux. I've never once had an issue with f.lux nor being in the startup list so if it's not there just reinstall the program.