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my problem would be solved if i would know where that bindings are saved

i have the last 3dnes version which dont have mapping input option i just downloaded the latest version to desktop launched it changed bindings and the bindings from previous version was still there
so i removed latests 3dnes version from desktop and even cleaned registry from 3dnes keys then downloaded latest version again and same problem there

only thing i can think of is if 3dnes creates some folder in appdata or some other location like that with settings

It is saved in windows registry so i'm sure it's a bug with some specific controllers. Let's try with another controller to see if the same thing happens again.