That's just bizarre. You could do what MyShiLingStar said and try the libusb-win32 driver, but both I and the developer of USB-Botbase recomment libusbK
Yep that's exactly what it does, you can fill your legit switch's island with something like nmts without having to go back and edit, then give said nmts to your friends (:
You could try matching switch versions or start a new save (backup your old one with jksv) and see if the error persists, and if it doesn't then you have a problem with your current save.
No matter what I try with libusbK. I can't get it to find my device. (Uninstall and reinstall, another USB, another cable.) I guess it is something about my old motherboard or something.
Then when I try libusb-win32 driver. It got pick up right away without any problem.
I use the libusb-win32 driver and have successfuly ported the usb code to ACNHPoker.
The only problem that I got so far is that if the switch goes into sleep in the middle of a connection, when I turn it back on, it would gives out the "not functioning error" when I connect to it again. Sometime it might require a restart of the switch for it to function properly again.