Gamecube controller stopped working after playing Wii U game (USB Loader GX)

[Azguk]

Hi,
So I was playing a gamecube game on my modded Wii U ( Wii U and Wii games on a HDD, Gamecube on sd card) with an official gamecube controller with the official adapter and then played a Wii U game. Went back to gamecube mode and the controller stopped responding. The Wii U pro controller works instead. I did not change any settings or add any games. Literally just switched from gamecube to Wii U and back to gamecube.
It was working perfect for the last two years.

The gamecube controller is working fine in super smash on Wii U. I have tried changing the settings in the loader menu and individual game loader settings, changing the USB-HID Controller on and off, native controller on and off and gamecube controller 0 to 4, I have tried all combinations and every time the Wii U pro controller works. I think the pro controller is getting priority over the gamecube controller. I have also restored usb loader's default settings and individual default game settings.
Does changing from gamecube (i.e. usb loader gx) to Wii U and back somehow corrupt or change settings? Because this is literally all I did.

Launching a gamecube game directly through Nintendont via the homebrew channel also does not make the gamecube controller work again.

Nintendont loader v6.489
firmware 58.25.32

USB Loader GX v3.0 Rev 1281 (e25c4e9)

Thanks.