I've got the exact same issue.
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@justgetflux sweet! I'm traveling and f.lux is giving me prompts, some detection would go a long way to resolving this!
Thanks for your note - that's a tough area to be on a solar schedule -as we move the other versions to a circadian schedule that will help you a lot I think.
Open f.lux settings, hold the CTRL key, and slide one back (one of them is locked but holding control, I think night can be made higher than day).
Pull day all the way down, hold CTRL, pull night up to your preference.
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