Im having issues with how f.lux handles dark mode; But I think it more has to do with us using a beta version of the OS rather than the app itself, because flux on El Capitan is working perfectly for me. What I would is that, when I toggle on dark menu from preferences > general, the menubar becomes dark but the dock and menulets stay the same (light mode). When flux handles this process during the day-night transition, menubar remains light but everything else changes. I just need to enter pref > ten and toggle dark menu manually. I installed a CLI dark-mode to troubleshoot and found that when the pref > gen toggle is used, the system remains registered as light
$ dark-mode --mode
Light
And I can enter original dark mode through
$ dark-mode --dark
It is kind of frustrating but that's what we get for using a beta OS until all the bugs are fixed. But this is under the assumption that the dark menu bar setting was already broken / incomplete in Sierra (didn't test the toggle before installing flux)