I have the exact same issue running v4.43, Win7 64bit and nVidia Quadro 410 on 21.21.13.7684 drivers.
The computer is locked overnight at work, and the night (or transition, unsure) color sticks when I come in next morning, long after my "earliest wake" time. If I close and start Flux again, the color temperature will properly be set to its day value.