Ah hah!!!
I got it!
the places where you have light in the darkness, you used a tile from farther in the tileset.
use the flood fill, and use one of the autotiles to fill in the light:
Then, flood fill the autotile with the very first tile, the blank one.
It should work then.
(Sorry if this doesn't make sense. It's really late here... The pic should help)