See this Comm Center thread by George Silvis et al. The flats actually start at AutoFlatConfig -> TwilightSunHi not 0 deg sun. Also there is a 2 deg "guard band" above TwilightSunLo ... if the Sun is that close to TwilightSunLo, dusk flats won't be done. Check these conditions for both dawn and dusk, and document this.