You say you save the map terrain, at the terrain folder, right?
You need to save it at FeralHeart>>media>>terrains>>WaterMill.
After that, you need to close all the tabs and press FeralHeart.exe
After that, you enter the map maker and stuff and press on the World.
Then, you need to delete the writing of the map terrain, to this~
{YourMapName}Terrain.png
Then click save or open. I cannot say for sure, do to me leaving the game. :P
Anyways. If you need further help, simply post here or Private Message me for further information of the Map Making.
I can help you, because before I left the game, I made loads of maps, so I know what to do. ;)
Good Luck, my friend! ^.^
Did you make sure the image size is even on both sides? (Ex. 513 x 513) If it's not a square then I'm afraid you'll have to remake the map.