In case anybody finds this post: this turned out to be an early sign of a problem with my graphics card. That eventually stopped working completely and I had it replaced; the f.lux issue hasn't returned.
There's a tiny little icon that appears on the bar across the top of your computer screen, to the left of the time. If you click there, you can set preferences, like "disable for full screen applications", or "disable for one hour". But you can also just plain quit out of f.lux when you don't want it on, and then start it up again by clicking on the icon in your dock or in your applications.
