OK, I have this problem with some Win 8.1 machines that have HighDPI scaling enabled (not whole screen displayed, mouse coords mapped incorrectly).
If I set compatibility mode in the .exe file preferences it *always* work on all machines without exceptions (so it's about HighDPI).
I did SDL_SetHint(SDL_HINT_VIDEO_HIGHDPI_DISABLED,"1"), it returns SDL_TRUE. Now, it seems to be working on some Win 8.1 machines, but not all (I have access to such machine so I'm sure it's not working)...
No clue what's going on...
I'm using SDL 2.0.1 + OpenGL.