For those of you using the x360ce program and the Mayflash GameCube controller adapter who are having trouble getting the game to pick up the controller:
1. Configure x360ce with the adapter in PC mode (the switch on the side of the adapter), then close the editor.
2. Start NIVA with the adapter still in PC mode.
3. While in the menu, switch the adapter to WiiU mode and wait until you hear Windows recognize the controller, then switch back to PC mode. You may need to reconfigure the "A" button in the editor and redo the process, however.
I also checked the boxes in the images in the third comment down here: https://github.com/x360ce/x360ce/issues/295 (the comment by tom2ross) . If the steps I outlined don't work, try checking the boxes shown in the photos, then hit "Apply/Synchronize Settings"; ignore any errors.
Also, if you're not using the Mayflash adapter, but your adapter has a way to switch between two modes, try that, too.
These are the steps I used to get it working. I hope this helps someone!