Okay, the short answer for this is hopefully the one that works. Go into your particle and objects files. When you export a map, it creates these dumb little duplicate files. Pesky, I know! They say _0, _1, _2, etc. at the end of the normal name. Delete these little buggers. All of them. Every last one, they will bug you like a mofo.
If that is not the solution, I did have this problem. I'm actually not sure what is was that fixed the problem, but it arose after the huge FH shutdown. My map two years in the works stopped working, along with every other custom map.
I had to uninstall the game. That's what worked for me.
I kept all of my custom items and my map files. I just had to go into map maker and create a fresh "starter" map with the same names, assign the terrains and heightmaps, and put all of the other files (objects and such) in the folder. Other stuff like music came after.
Perhaps that may help you? Be careful not to delete anything too important/irreplacable.
