With multiple monitors, tabbing from a full-screen game has no transition time

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I recently got a second monitor and noticed this issue. Normally, things work like this:

Be in a normal desktop app - say, Chrome. f.lux is active.
Alt-tab to a fullscreen/borderless windowed game. F.lux turns off using the standard transition time (slow, in my case).

When I plug in a second monitor, f.lux will remain active for a moment before instantly turning off. It's rather jarring and not nice on the eyes.