Ambrosios

Why are you using 64,144 for the tile width and height ? You should use 64,128 instead.
 
Check my tutorial on tilesets (a new version will be coming tonight or tomorrow with better explanation for tile creation) :
 
http://theindiestone.com/forums/index.php/topic/6312-custom-tilesets-and-fences-for-pz-map-editor/

Hehe, I'm happy that I tested it because my assumptions were wrong.
 
They are not layers, but floors. If you put a lot on level 1, you can access it only if you climb one floor.