I figured out the issue. Windows 10 has a new "feature" called "Fullscreen Optimizations", which forces every app into borderless windowed mode (!?!). This also explains why all of my games have been getting significantly worse performance since the update.
I haven't figured out a way to disable it globally (none of the suggestions online work), but you can disable it on a per-app basis by finding the executable, right-clicking --> properties --> compatibility --> "Disable Fullscreen Optimizations". After doing this, flux will disable correctly for that application.