ID:161586
 
There is something weird happening when I run my game. The map is fine and there are no compile errors. The dark grren is supposed to be over the light green. Instead it is making it black.

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I have no clue how to fix this or what it is.
It looks like the light green turfs are getting replaced by the edges of the dark green grass. Are you creating turfs at run time and locating them there?
There's only one turf per tile, so when you place a new turf on top of an old one in the map editor the old one becomes an underlay. Underlays will have the same icon state as their base atom, so if the dark green grasses state is "left_edge" and the light green grass below it also has a state of the same name it will be set to it. In the current example, it will likely hide the underlay completely. I'd prefix your turf icon states with the icon's name (eg: "left_edge" in dark_grass.dmi becomes "dark_grass_left_edge") in your .dmi files.