I think this is a bug completely cause by the patch with no real fix for it.
I have no why it happens or how to make it stay away. But for me it seems to happen everytime I edit the scale of the map in the world tab, or some other change there.
If you got a correct heightmap made, and all the values as you want them, you can go into the terrains folder. Find the folder for the map you're making, enter it, and then open the (mapname)Objects file, and remove all of the text in there.
It will delete all the objects inside that map. and you are free to start adding things. Though, as soon as you edit something like the height inside the world tab again in the map maker, all the random items from another map will plop back.
Not sure what happend, but the new patcher messed up the map maker just a tad bit.