Use more layers when I use tiles?

Hello

So I am trying to create some automated tiles and pyxel is the best for this job. But this works only on one layer. When I use a second layer the tiles not aren't working.

in this first picture http://prntscr.com/mj31ce its working fine

now here it just doesn't work http://prntscr.com/mj31rn

so what do I do wrong?
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