Odd... It could be a file corruption, but I'm not sure.
Map Maker can be a little bit finicky sometimes, but what you could try is opening up your map in Map Maker, then renaming it so it becomes a brand new file in your game.
Then, press Export.
It should reset the files and make things work a little better for you. But, if that doesn't work, let me know. I'll be hanging around to help ya out if you need it. ^^
-- Also, make sure you have all of the updated FH patches. (This probably isn't it, but I just want to have that out of the way.)