Intense blue flickering (MBA, '13, El Capitan)
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Yes this is related to Apple's new "auto brightness" feature which also adjusts midtones in bright rooms.
And it definitely happens on our MBA with auto-brightness "on" in settings, and it goes away otherwise (may take a reboot also?)
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I've just installed the 36.5 version, and seems that the bug is solved.
Thanks!

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@lpuerto Damn! It returned! (the flickering)
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The ones with 10.11.2... have you reported it to apple? Seems that it's also an apple problem :)
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Since there are two reports of MacBook Pros not being affected, I'll add that my Mid-2014 Retina Macbook Pro running 10.11.1 IS affected. It has integrated graphics only.
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Yes in the newer betas we are seeing it anytime the Automatic Brightness feature is on (or when it's recently been turned off).
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I am on the same setup, and with the same problem. It was so annoying I quit flux. But that was even more annoying.
I disabled "Automatically adjust Brightness" in Display prefs and sofar sogood.
OSX 10.11.1
MacBook Air (13-inch, Mid 2013) -
Is there anything that can cause it to re-enable itself? I could've sworn I'd disabled that, but I looked again and it was enabled. Just disabled it and no flickering (so far).
FWIW I'm on a Late 2013 13" MBPr with 10.11.1.
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@whatismyusername that's frightening! did you reboot?
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@lorna Sorry, just remembered it was the "Adjust keyboard brightness in low light" setting I had disabled. False alarm.
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Wow, I didn't even know that was a thing now, ha. Whew.
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