f.lux doen't start after booting

I've experienced the same issue.

Changing the Exec field in ~/.config/autostart/fluxgui.desktop to sh -c "fluxgui >> ~/logflux.txt 2>&1" would allow you to examine the reason for the failure to start-up.

I've got the following traceback:

Traceback (most recent call last):
  File "/usr/lib/pymodules/python2.7/fluxgui/fluxgui.py", line 381, in <module>
    app = Fluxgui()
  File "/usr/lib/pymodules/python2.7/fluxgui/fluxgui.py", line 17, in __init__
    self.indicator = Indicator(self)
  File "/usr/lib/pymodules/python2.7/fluxgui/fluxgui.py", line 149, in __init__
    self.setup_indicator()
  File "/usr/lib/pymodules/python2.7/fluxgui/fluxgui.py", line 162, in setup_indicator
    'gtk-icon-theme-name')
ValueError: could not find setting

Apparently, this is a known bug. However, a workaround is provided by @sricks:

This bug is still present. BUT you can fix it by modifying line 162 of /usr/lib/pymodules/python2.7/fluxgui/fluxgui.py.

Change the theme = line to look like theme = 'ubuntu-mono-dark'. If you don't have that theme installed, no problem, it just uses a default. Lines 161, 162, and 163 should look like this:

if gtk.gdk.screen_get_default():
    theme = 'ubunto-mono-dark'
    if theme == 'ubuntu-mono-dark':

This fixed the issue for me.