I thought I had Wiinusoft all set up. It was working in the settings menu, but when I opened Minecraft, the controller (Wii U pro controller) didn't work. Only the mouse and keyboard inputs worked. I went back to my settings menu and the controller worked there. I opened a web browser and it didn't work there. I went to the start menu and it worked there.
Is there any reason why it would work in the windows menus, but not in the programs?