Hardware GameCube controllers not working only in Smash

[NFates]

So, GameCube controllers (2) aren't connecting, but only in Smash. I tested Cuphead and Mario Kart 8 Deluxe, and they work flawlessly, but in Smash they won't even show up. Tried restarting the console and game, changing controller ports and USB ports, and reinstalling update. Doesn't work.

Things to take in account:

1- They worked before, but now I installed the 3.0.1 update and they don't anymore.

2- The game is a cartridge.

3- Running FW 8.0.1 and Atmosphere 0.8.9 with sweet patches.

Thanks for any input!

EDIT: The "only" in the title is not supposed to be there, lol

 

[NFates]

Further development:

Already "solved". I had the hid-mitm module on the SD card. When I deleted it, things went back to normal. Before this, I downgraded to Atmosphere 0.8.8 (no module) and worked, updated to AMS 0.8.9 (no module) and still worked, then put ldn_mitm and hid-mitm and didn't work. When I deleted hid-mitm, the controllers worked again.

Maybe the guys at Team AtlasNX would like to test this out. It was version 0.1.1.