It either sounds like a image size file error, or you forgot to flatten/merge layers after you were done creating the map.
I don't know what program you used to create the file, but if you created the map with multiple layers, it HAS to be one layer ONLY. Have one saved as the program's editing file, and another saved as a .png. This way you can test a map and easily go back and edit it if anything appears out of place.
Try to make sure that the Alpha layers are off as well (google that too, depends on your program), and that the actual mode is in grayscale (again, google :I ).
Also try looking at the Manual here on FH, in the Map Maker section (Click!):
Height MapsTerrain MasksGetting a Map In-GameHope this helps!