Ok, i think i found the trick.
I downloaded a unity demo game, which works fine in 3D. At start i can select resolution and windowed mode (or not).
If i start in windowed mode and go to full screen with alt+enter screen blanks for 2 seconds, and 3D will be ok.
With your app changing mode with alt+enter i don't see black screen, the switch is immediately between fullscreen and windowed mode.
So it seems you don't use exclusive directx mode, which is needed for 3D, and i think this was the problem with my vsync tearing issue too.
"DirectDraw Exclusive Mode, an application takes exclusive control of the graphics hardware. This is useful for applications such as games" :)Can you compile a new version with exclusive fullscreen mode?
Build&run: don't select stereo and don't select windowed.