When I open the program, How to automatically hide it?
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Every time I click the Close button.
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How do you make the Notification Area icon disappear? You can't. If you have more than one Notification Area icon that you want to hide, then you can put all of them in the Hidden Icons area, but the icon cannot be hidden otherwise.
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Oh, is it popping up every time you boot? Look closely at the program, you'll see it's asking you to set your location. Set it to a location near you to get proper sunset and sunrise times, they also vary by season!
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I am now thinking that you're talking about when you don't have f.lux open AT ALL, and you go start it up manually. Yes, f.lux doesn't start minimized in the Notification Area unless it starts with Windows. It starts open. You don't have to click the close button, just click somewhere else and it disappears when it loses focus.