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I've been using f.lux for a while and absolutely love it.

It works correctly on my laptop and also on my external screen. However, when I try to use both of them simultaneously - the magic of f.lux brightness adjustment disappears and I'm back to default settings.

Is there a way to sort it out somehow?

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In my case this topic helped: https://github.com/Kilian/f.lux-indicator-applet/issues/16

Herf prepared a brilliant patch for xflux which has to replace the original /usr/bin/xflux and it works like a charm.

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