You know, I was just looking in my shell and ran across a possible "magic" env variable in my configs that I had commented out a while back.
#Multihead fix for SDL
export SDL_VIDEO_FULLSCREEN_HEAD=0
I use zsh, so that's set up for zsh.
If I remember correctly, what this does is set full screen sdl on only one monitor. Primary would be 0, secondary 1, etc...
Remember that after setting the variable, you either need to log out and log back in, or start a new shell, and run the game from that shell, or else it won't take effect.
HTH