Arty, can you share your PropRandomizer script? The chunks are not spawning multiple times (only 1 chunk is appearing in your Hierarchy window). Your props are spawning multiple times.
Hi, uhm, eventually i fixed it. The problem was the layer in each chunk was set to nothing and in map controller theterrain mask was also set to nothing, so i changed it to terrain, and now it works perfectly fine. Sorry for bothering.