I had this issue as well. For me, it was fixed by deselecting "Disable>for fullscreen apps." With that setting on, f.lux would be at daylight on an alt-tab out of a game, and it would transition (at whatever transition speed had been set in the preferences) back to my nighttime color. With that setting off, colors would still be normal in the game (i.e., f.lux was disabled in the fullscreen game anyway), but the transition back to nighttime color would be instant on an alt-tab. Hope that helps.
And for the developers, you may want to make that transition (when leaving full-screen if the "Disable>for fullscreen" mode is on) instant, though perhaps you have your reasons for making it slow.