Pressing Alt-Enter with Allow Fullscreen Switch causes Default is Native Res to set true?

Hi,
Trying to figure out some odd behavior with resolution/screen modes.

We've unchecked Default Is Native Resolution and checked Allow Fullscreen Switch, however when we start the game, if you quit straight back out without setting resolution, registry shows Default is Native Res setting to true.

Equally if I hit Alt-Enter to switch screens, I also see Default is Native Res set to 1. There's nowhere in our code setting that, so I'm thinking maybe Unity does this to make sure there's some smooth change over in screens/from windowed to full screen, is that right?

Also I'm making sure to delete registry every time.