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.
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.