Happened to me too, It must be from a different version of photoshop.
What I did though is just select an 8x8 pixel section, and make sure it was a multiple of 8 away from the edges. then i filled in that selection with black on the "Routes Background" layer.
In the end, it doesnt matter how you draw the map, as you'll save all the layers as a png.
Now for a question:
In FR, after you play Cinnibar Island, you get invited by Bill to that group of islands with the internet connection problem.
At that point your map gets another button on it for changing maps.
How do you incorporate this into a custom map?
-Draw it of course.
-Then would i cover it with "3" tiles in the NTME pallete editor?