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maybe i just miss the point but what clear button will do? i got no keys binded but 3dnes acts like there are key bindings

so for me just removing that bindings would solve the problem

its like aside from normal bindings that i can make in emulator it have some bindings hardcoded

well i didnt think about it but i in fact have here like 10 controllers (was testing/looking for perfect one) i need to try them out if they have same issue

There is always an initial binding. When you create a new binding, normally the old one will be removed. Maybe this is a bug with a specific controller that the old one had not been removed. A clear button will make sure every mapping will be cleared then you can assign all new mapping one by one. This is a workaround for your problem i guess.