HI!
I've been poking around for months at our libSDL issue where the fullscreen window is shifted down.
Finally I found changes that fix it in everything i've tried.
diff: include/SDL_config.h
http://0x0.st/i3qf.h
diff: /src/video/x11/SDL_x11video.c
http://0x0.st/i3qO.c
Video: Arx Libertatis (OpenGL-ES)
http://0x0.st/i3qs.webm
Would be happy to hear if they work for you as well.
Cheers!