After a while I just gave up and uninstalled f.lux. Instead, I created a 4500K white point copy of the default color profile and manually switched to it at night, which seemed to have the same effect. It also prevented those big flashes whenever switching to and from full-screen apps.
I'm grateful that f.lux has pushed this issue to the point of getting traction as a built-in feature from Apple (and I do hope Apple brings it to OS X at some point), however unless f.lux becomes open-source, I don't plan to reinstall it.