@herf Well, this is odd, and I'm not 100% sure why things changed back to working correctly. I had restarted the laptop several times and the bug remained.

Then I happened to run Cocktail's system cleaning/maintenance routine, restarted my MBP and noted that the f.lux logo started showing correctly again (white logo on black background) in Bartender 2's menu bar as well as the regular MacOS menu bar if I left f.lux there.

I'm still at a loss for this bug, but the pesky issue has gone away. Something corrupted in a cache that was cleared by Cocktail, perhaps?

I'll leave this here as a hint if anyone else runs into this bug after installing MacOS Sierra.

@Become1 said:

I removed the compleet program

I removed the compleet program

@cgm2016 you can uninstall by quitting f.lux (in the menu to the left of your system clock) and deleting the files. You may want to check if your MBP is one of the ones affected by a video driver problem, this isn't normal behavior with f.lux: www.macrumors.com/2015/02/19/2011-macbook-pro-repair-program-apple/

@Merrill in the upper right corner of your mac (just to the left of your system clock) you can access all the preferences.

Reinstall seems to have done the trick. Thanks!

bumpppppp

The "OS X Dark theme at sunset" option seems to be not functioning in MacOS Sierra, can anyone else confirm?