Here's how I got windowed fullscreen to work. My resolution is 1920x1080. I edit ddraw.ini, set HiResMode=0 to disable the built in high resolution mod (I will setup the classic high res mod later instead). Under [Graphics] I set Mode=6 to enable the sfall's fullscreen windowed mode. I set GraphicsWidth=1920 and GraphicsHeight=1080 to match the native resolution of my monitor. I also set TextureFilter=0 because otherwise everything is too blurry for me, but it's up to your preference. Next, I edit f2_res.ini and set GRAPHICS_MODE=2, SCALE_2X=0, SCR_WIDTH=960, SCR_HEIGHT=540, COLOUR_BITS=32, WINDOWED=0, WINDOWED_FULLSCREEN=0
Please note that I have set my native resolution in sfall (1920x1080 in ddraw.ini), but half the resolution in the high res mod (960x540 f2_res.ini). This way the game runs in full screen windowed mode at my native resolution, but all the graphics in the game are scaled 2X.