This same thing happened to me. It doesn't happen with worlds I download until I add them to Minecraft. But I did notice something strange. I loaded Greenfield (Minecraft's Largest City) into mine-imator after adding it to Minecraft and it was blank. But when I zoomed out the rest of the map started loading except every block that was within a 1000 block radius of the player. (What I am saying there is basically a giant hole in the world)