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Which platform are you on? f.lux on OS X works just fine across many displays.

Yes, I should have mentioned my platform. It was Ubuntu Maverick or Lucid. I haven't checked it on any newer version.

Yes, RedShift does support that. I've just tested on a laptop with an external monitor attached.

I can confirm that.

Even the app-indicator version doesn't support 2 monitors? What setup is your dual monitors? I'm trying it out, I don't use gnome-panel applets, those bastardly things.

Flux definitely works on both of my monitors here just fine.

I haven't been using f.lux since I learned about the flaw - it would only work with one of my monitors on Ubuntu Maverick (or Lucid, I don't remember now).

I'm now happily using redshift and it does work with two monitors.